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Because pony physics are a bit weird, guesses will creep up. If you have guesses on other things then:

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The universe runs on friendship.
Literally. The physical laws of the universe is actually thinly held together. They break down constantly and require maintenance. Usually, they are held stable by magic. However, over 1000 years ago, Equestria figured out how to harness the power of magic, turning their realm into an Utopia, but at the cost of physics within the land slowly decaying. The royal family, possible the then young princess Celestia, gathered all ponies together, and organized them, taking over the responsibility of ensuring the season turns as supposed to, as well as such things as gravity and speed of light. This also nicely helped solve the recent unemployment problem.

Clouds are actually gaseous non-newtonian liquid instead of water.
Non-newtonian liquids become solid when pressure is applied to them, and allows one to walk on water if done carefully, as seen in several YouTube videos. Clouds in Equestria are gaseous forms of these liquid, which allows them to remain airborne but still have enough liquid to be solid when comparably-light pegasi walk on them. The spell Twilight uses in "Sonic Rainboom" is really a spell that reduces earth ponies' weight to that of pegasi.
  • Also explains why repeatedly stomping on a cloud causes it to dump its water onto whatever is below it.
  • This also explains how Rainbow Dash was able to break her friends' fall with a compressed cloud in "Wonderbolts Academy", unless you believe that Twilight cast the cloudwalking spell on them again.

The reason the ponies need to control the plants, animals and weather is because Discord is imprisoned.
Discord was/is the physical manifestation of Chaos... which isn't just "everything goes wacky", it's a necessary attribute of physics. Much as superheated pure water can't turn to steam until an outside force perturbs it or introduces a tiny contamination, without Discord's presence, Equestria doesn't have enough natural chaos in it to trigger the formation of clouds, or of raindrops/snowflakes/ice crystals, or the shifting pattern of winds, or the ebb and flow of plant or animal lifecycles. But given a choice between having to crank the ecosystem over manually or having a mad god loose in it, the ponies made the obvious choice. It's also an explanation for the Everfree... it's the last natural source of Chaos left in Equestria, and so is kept as a nature preserve.
  • Jossed, as Discord has been reformed and weather ponies are still seen managing clouds.

As opposed to the above theory, The reason the ponies need to control the sun, the moon, and the weather is because Discord went rampant all those years ago.
Their world used to work like our own. However, it never quite recovered from Discord's reign, and now the intervention of alicorn princesses and regular ponies is the only thing keeping the balance of nature and preventing the end of all life. And it's been so long that everypony thinks that's normal now.

The Apple Trees (Malus spp) in this show work the way fruit trees in Animal Crossing work.
With the exception of the few episodes that take place in winter, there are always big ripe apples on the trees, even on the summer solstice. Even though Applebuck Season is ostensibly not all year. They probably grow from seeds in a few days and grow new apples every three days.

Ponies have access to electricity...
...but NOT to fossil fuels. Thus the existence of a hydro-electric dam and various minor electric appliances is possible, but the existence of cars and other major industries as we know them is NOT possible. This is not a case of environmentalism, mind you, but a simple matter of discovering electricity before gasoline (although environmentalist ponies are probably happier for that).
  • Not that they'd need fossil fuels, since they DO have access to everything they need to generate electricity. They have windmills and water turbines, and it's not hard to imagine that solar panels exist. Unicorns have been seen using their magic to power machines. Organic waste can also serve as a fuel source. Even if fossil fuels did exist, there are enough alternatives in place to make drilling for them pointless.
  • If the world is assumed to be relatively young, created by magic or gods sometime in the last million years, there are no fossil fuels to find. The ecosystem hasn't been around long enough to make any.
    • That's kind of mixing your paradigms. If the world was indeed spontaneously created ex nihilo at some point, there's no reason it couldn't have come with fossil fuel depots (or functional analogs if one wants to quibble about the definition of "fossil fuel") already included.
  • Jossed. In "MMMystery on the Friendship Express", the conductor is shown shoveling coal (which is mentioned in the dialogue as, indeed, being coal).
    • Equestria could still be very young. "fossil" (carbon based) fuels can be formed very rapidly, under the right circumstances. Coal, for instance, can be created in a laboratory setting, as can diamonds — it just takes heat and pressure. Which may also be why diamonds are valuable — other gemstones are ridiculously plentiful, yet diamonds are referred to as extremely valuable (Best Night Ever, Return of Harmony) — presumably other gemstones grow due to magic, like crystals, but diamonds, being pure pressurized carbon, do not.
      • There is also the matter of the internal-combustion-engine powered sewing machines that Applejack comes up with in Apple Family Reunion. However, this is easily explained by the fact that small, high-rev engines can run on other volatile liquids than gasoline. such as, say, ALCOHOL Likewise, larger Diesel engines can be made to run on vegetable oils: current human society uses petroleum because, for the moment, it's easier to get and more energy-dense. (such was not the case even in modern human civilization: when coal-fired steam engines ruled the rails, it's because coal was easier to get and prepare for use than oil.)
    • Could it have been charcoal?

The dam in The Mysterious Mare-Do-Well produces magic
Almost exactly like a more local version of the Lux Font of the Rac Conan Diamh(sp) in Tales of the Questor, right down to the use of invisible ley lines rather than cables on poles to transmit the power.

That's why the locomotive in "Over a Barrel" needed a team of earth ponies to pull it, and that's why the ponies working the construction equipment in "The Mysterious Mare-do-Well" were all earth ponies. The locomotive was pulling the train, but it needed a team of earth ponies galloping before it to power the boiler.

The main power source for magic-run machines are gems.
We've seen them used for a lot of things already (decoration, food source for dragons, presumably they have monetary value). So for gems being a source of power for machines wouldn't be a huge stretch.

Equestria is on the verge of an Industrial Revolution
But they have no incentives to automate because labour is cheap enough that it's not cost-effective to invest in sophisticated labour-saving gadgets. We see that they have some factories that make use of machines to create goods, but the products are shoddy and they aren't able to compete effectively with handicraft-workshops for high-quality products at the least. More importantly there's no hint of any mechanisation of agriculture, an important thing given that the balance of services:manufacturing+mining:agriculture is usually 1/3:1/3:1/3 in pre-modern economies. In the real world automation gradually came about as a result of increasing labour costs at a time of rapidly growing local and regional trade. Inter-continental oceanic trade helped a bit, mostly for the way it resulted in Joint-Stock Companies and Investment Banking, but the vast bulk the growth in trade was just regional and local courtesy of increased investment in roads and particularly canals. We have yet to see any other states besides Equestria, so it's quite possible that somewhere else is beginning to use more tools and machines because it allows them to save on wages.
  • Well, they do have video games as of "Hearts and Hooves Day"
The solar system in which Equestria exists is heliocentric/Celestia and Luna actually don't move the sun/moon, but rotate the Earth on its axis.
In the intro for the show (here), there is a glass window on the right of Celestia that seems to depict an Earth-like planet in a heliocentric orbit — although we cannot see the orbit of the Earth-like planet, the small, ringed planet in the upper left corner does seem to depict its orbit around a sun (whose existence is implied by the rays in the image), so we can safely assume that the Earth-like planet is also orbiting around that sun. Assuming that the Earth-like planet is a portrayal of whatever planet on which Equestria exists, this strongly suggests that the Equestrian solar system is in fact heliocentric.
  • PS. After watching bits of Return to Harmony, more stained glass windows seem to suggest a heliocentric orbit. If the Equestrian universe is in fact heliocentric, this ultimately means that Celestia and Luna are rotating the Earth on it's axis, instead of moving the sun/moon. Alternatively, Celestia and Luna's jobs are to keep Earth from crashing into the sun (Celestia) and the keep the moon from crashing into Earth (Luna).
  • Raises the question, though, why knowledge of what the princesses actually do doesn't seem to be more widespread. Why, given the state of astronomy in the setting (with our own Twilight Sparkle being an astronomy nerd not above lecturing her friends for their educational benefit herself), is the old "their magic raises the sun and the moon" story still around and apparently unchallenged if that's not in fact what happens? (Sure, under another regime I could easily see that sort of knowledge getting suppressed if it's inconvenient to the rulers. Neither princess strikes me as the type to do that here, though, especially when whatever role it is that they're playing in maintaining the day/night cycle clearly is vital and thus arguably something they'd have reason to be proud of...)
    • I think that this is merely linguistic convention. We must not forget that we ourselves say that the sun “rises” even though we know that this is not true. It should also be noted that the moon does indeed move.
    • Assuming the window displays a heliocentric system requires quite a stretch and a good dose of artistic license to boot. At best it resembles an abstract portrayal of the earth and sun and other heavenly bodies.
  • Perhaps the orbital mechanics of their solar system would not function with an outside force-from Princess Celestia and Luna, or even the Elements of Harmony. Possibly due to gravity wells in all the wrong places.
    • What does "gravity wells in all the wrong places" even mean, exactly?
  • There is a serious issue with this, namely the scene in "Twilight's Kingdom" where Twilight has to raise the sun herself, and the sun is visibly wobbling as she does so. Now, let's assume that physics in Equestria, including gravity and inertia, work as they do in our world except when shown or stated not to. The problem is what would have to happen to make the sun "wobble" in the sky like that: if the sun is not moving and only the planet is, then the planet would have to be the one jerking back and forth as Twilight works her magic. Most of these guesses (besides this one specifically, I’ve seen this idea tossed around on several occasions in other fandom websites) boil down to hypothesizing that the Equestrian system works like our solar system, so let’s use that as a model: the Earth rotates at a speed of over a thousand miles per hour at the equator, slowing down as you approach the poles (we don’t feel the speed because everything on the planet, including the atmosphere and oceans, is moving in the same direction at the same speed). If you just rotated the planet in the other direction (which is what would make the sun "move" directly east), then everything on the world's surface would still be moving west at the same speed as before. This would mean that a) everything less firmly rooted than a typical bunker would be violently hurled west at speeds of hundreds to thousands of miles per hour; b) the entire planet's surface would be scoured by winds blowing at the same enormous speeds; and c) the oceans would literally slosh over their western shores like the water in bathtub being jerked to the side. If the planet is also spasming back and forth in random directions, all this would be compounded by the random and sudden changes in direction of movement. Obviously, nothing of the sort happened.

    TL;DR, in a heliocentric model, the sun jerking back and forth in the sky would require the planet to itself jerk back and forth, which due to speeds required to make a planet the size of Earth rotate fully on itself every 24 hours and the law of inertia would in turn mean that everything on the planet itself would be hurled in random directions at unimaginable speeds and/or thrown into outer space.

    When comparing theories, the one that relies on the fewest unfounded assumptions is the likeliest to be true. In order for Equestria’s system to be heliocentric, we need to assume:
    • a) That the canon, as presented in the show itself, is factually wrong. Basically, that whenever canon materials have said that Luna and Celestia raise the sun, said canon materials have not been telling the truth about how the world of MLP works.
    • b) That Celestia and Luna are either flat-out lying about how their powers worknote  or fundamentally do not understand how their own powers, which Celestia at least has been using daily for a millennium, work, despite being well-informed about magic otherwise.
    • c) That Twilight either lied about her own experience in raising the sunnote  or also fundamentally did not understand what her magic did, despite she too being very well-informed about magic otherwise.
    • And d) that there was some method for suppressing inertia while the planet was being moved or that inertia simply did not apply in this situation, despite neither option being stated, showed, hinted at or implied in any way.
    • By contrast, the geocentric model where the planet sits still in the middle and the sun and moon are moved around it simply requires the assumption that what the show has stated to be true is true.

Equestrian apples undergo fermentation while still ripening on the tree.
This not only settles the whole alcoholic vs. non-alcoholic cider question, it also explains why the Apple family's apples and related products are so popular all over Equestria. Just as appears to be the case in real life, ponies are as a rule less affected by alcohol than humans...but they're still quite capable of enjoying it.

Rocks, jewels and gems in Equestria "grow".
Jewels and gems occur only a couple of inches below soft ground which makes no geological sense, there never seems to be a shortage of them despite the fact that dragons regularly eat them in large quantities, Spike was "aging" a ruby to perfection and Pinkie Pie came from a "rock farm" suggesting that something about the rocks, jewels and gems in Equestria have properties that allow them to gain mass and multiply without having to use geologic (as in volcanos) amounts of force.

A number of theories have been proposed:

  • Gems and rocks from the rock farm are actually some sort of plant, fungus or some unheard of mineral-based organism similar to the two.
  • Mined ores absorb magic present in the atmosphere to gain mass: Based on this Ask Tumblr post.
  • Gems are a solidified form of magical energy (or "mana") that accumulate overtime to form jewels and gems.
  • Gems have properties similar to Tiberium and convert soil and rock around them into more of themselves.
  • This strange property was caused by artificial means a very long time ago. Either by accident or on purpose.
  • Gems can be 'farmed,' but only by Earth Ponies, everyone else has to mine them the old fashioned way.
  • Gems and rocks grow from minerals and elements accumulating as a natural magical process.
    • This occurs more abundantly in some areas (like the spot where Rarity goes gem mining) than in others — perhaps the magic is stronger there, or upwellings of water or magma bring more minerals to fuel growth. Earth pony magic can control and direct this process to make harvesting desired minerals or rocks more efficient or gainful, hence rock farms.
    • As a further theory, the reason rock farms don't grow gems is either a) large, pure gems require more energy or materials to grow than rocks do, meaning they’re not cost-effective to cultivate, or b) earth pony rock farmers just don’t feel like farming gems with no practical use when they could be growing useful ores and building stone.
    • A bit of evidence for this being a natural process is the existence of a large species of gem-eaters, the dragons. Logically, they would have to have access to naturally occurring, self-replenishing sources of gems — they have to keep themselves fed somehow, and given what we’ve seen of them it's... unlikely... that enough of them are peaceful farmers to supply an entire species of house-sized reptiles with food. Obviously they can steal from the ponies, but they would still have had to eat before ponies developed rock farming.
    • With the existence of the Crystal Empire and King Sombra, it's possible that all of the "gems" seen in the show (the ones Rarity and the Diamond Dogs dig for / the gems dragons eat) were all created by magic, which would explain their post-cut appearance. This might also explain the Pie's rock farm: by concentrating their magic into the ground they can alter the molecular structure of the rocks into something valuable a la Fullmetal Alchemist. As for why these magically created gems are burr din seemingly random place, the answer could be anything from natural poets of magic to leftovers from an long forgotten war.

The pre-cut gems are actually some form of natural sugar crystals.
Equestria has plants with a higher concentration of natural sugars because of how their sun works and the high magic field that surrounds both the pony-run biomes and the Everfree Forest. In areas that once had sugarcane, uncontrolled tall grass, or grass farms but were abandoned or partially burned, this sugar seeps into the groundwater where it forms seeds and collects into crystals. Dragons are able to digest gems because of their internal combustion systems, which run on several different fuels, including sucrose and ethanol, though the sucrose is probably mostly converted into ethanol for fire and glucose for biological use. Ponies could eat gems, but sugar cubes, sugary baked goods, and hoofmade rock candy are just as tasty and less likely to contain unpleasant-tasting, harmful impurities that make the crystals less water-soluble or be sharp enough to cut up a pony's tongue. These impurities determine what name the ponies use for the gem, and how the gem reacts to light and fracturing (blue and indigo gems, for examples, are "diamonds", as well as regular carbon-crystal diamonds; other types of crystals may exist with the name duality in Equestria, may only exist as the sugar gems in Equestria, or may exist only as the lithic gems as in our world, depending on the type of gem in question). Rock farmers farm these gems (probably among other things, such as being slang for quarriers who surface-mine fieldstone instead of digging quarries) by buying up small gems and adding the appropriate impurities and sugar solutions to the earth to best promote the formation of large, quality gems. In a pleasant coincidence (assuming it even is a coincidence), this means Pinkie and her immediate did fit in the same sugary-treat theme, and neither Mr. Pie nor the Pinkie-esque Granny Pie were necessarily black sheep. This even makes Pinkie's parents' occupation even more fitting to their personalities and place in Equestrian culture: Their entire job revolved around a sugary confection that couldn't be eaten, the perfect (*hrm, hrm*) item/crop/focus for a family that's too bland for its roots and, at its most extreme, refuses to accept fun as something healthy and normal.

The train to Appleoosa was pulled by Earth Ponies because the "engine" was some sort of work amplifier rather than a straight-up engine.
It uses some system (burning charcoal-encrusted enchanted gems? Water-cooling an enormous, enchanted gem that heats up when its spell is active?} to act as an inertial damper and less-than-1:1-effectiveness levitation spell so that a small team of Earth ponies can pull the train and its passengers without noticeable reduction from their normal running speed. For them, it feels like merely co-flying a kite on rails with the kite-string attached to their yokes instead of hauling something. The last cart on the train slowed down so suddenly when it was disconnected from the rest of the train because it experienced a sudden but possibly incomplete reduction of the effects of the spell (possibly incomplete depending on what the spell actually does).

Ponies use a ridiculous amount of caloric energy even without magic using up calories.
They're four-foot-tall equines with heads relatively far larger than even humans. Even if they're not any smarter than humans on average, they still seem to have larger brains, and probably have muscle density on par with that of real-life horses and ponies, or even better, in addition to their stockier builds and narrow but powerful necks (as shown when ponies suffer Amusing Injuries and do things normally reserved for Automaton Horses like the ponies pulling the train to Appleoosa). This is how and why ponies (and not just Pinkie Pie) can gorge themselves on sweets and sugary baked goods without getting sick. It's even possible that they don't digest plant matter as efficiently as horses in our world, and they use some of the extra energy from the sugary treats to power the extraction of nutrients from hay, leaves, and stems while still being able to stomach things like ice cream and (possibly) ham sandwiches.
  • Larger brains? Look at their eyes, and then imagine those are spheres rather than simply two-dimensional camera lenses. They hardly have room to have a brain at all...
    • So? Brain size and intelligence are largely independent.

Equestria has mechanical water tanks that act as the lead Tank for wilderness rescue missions.
That's the sort of tank for which Rainbow Dash named Tank, regardless of whether or not artillery tanks exist in Equestria.
  • Or they could have tanks armed with water cannons.

Zecora didn't really cure the cutie pox
There is no actual known cure for the Cutie Pox. The Heart's Desire just gave Apple Bloom the condition and Zecora knew how to undo the effects of the plant.
  • Alternatively, Zecora's cure amplified the effect of the Heart's Desire potion enough to power another wish. And since Applebloom now intensely desired to be rid of the fake cutie marks, that's what happened.

There are no dominant and recessive pony types.
"Baby Cakes" seems to imply (though not directly state) that Earth pony gene is dominant and the unicorn and pegasus genes are recessive. And it appears that the vast majority of the pony population is Earth. However, it's evident in fanon that many bronies prefer to be portrayed as pegasi and unicorns, making earth ponies a fanon minority. Thus, if Earth ponies really were the dominant trait, we should be having a lot more Earth pony ponysonas, which is clearly not the case. And therefore, my theory is that pony parents can give birth to different pony types only if there they had an ancestor who was a certain pony type, and the probability of being born of a different pony type from one's parents is inversely proportional to the familial "distance" between ponies.For example, if a unicorn marries an earth pony, and the unicorn's grandfather was an pegasus, there is a small but considerable chance that their foal will become a pegasus. The chance of said foal becoming a pegasus becomes even smaller if the unicorn's great-great-great-great grandfather was a pegasus. This doesn't happen often usually because ponies of the same race prefer to marry one another.I know this is based off the fan community and shouldn't be taken all that seriously, but I like to think that, if everyone in the real world had an Equestrian counterpart, it would be really weird (not to mention disappointing) for many bronies to present themselves as, say, pegasi, only to actually have an Earth pony counterpart in Equestria. (Again, this is based on the baseless assumption that there really is an imaginary land called Equestria, but, hey, it's called Wild Mass Guessing for a reason, right?)

Unicorn cannot remember casting teleportation spells
Theoretically speaking, teleportation could function as a pony magically inverting their mass/gravitational field. This would make them a living tachyon, allowing near-instant transport faster than light. This would, as per special relativity, physically move their particles back in time during transport, essentially deaging them a few seconds, meaning they have no memory of casting the spell. They pass it off as a quirk of the spell, and none of them realize they are dead due to lack of the needed technology to establish something that accurate.
  • Why would they be dead?

On the Relative Power Levels of All Characters in Equestria
This is a list of characters/setting elements in Equestria, organized by magnitude of power. Feel free to add your own notes and observations on the topic.

The base list, which I have come up with, goes as follows:

  • The Elements of Harmony
  • The Power of Love (i.e. Cadance + Shining Armour)
  • Discord
  • Nightmare Moon
  • Celestia
  • Luna
  • Cadance
  • Twilight Sparkle
  • Shining Armour
  • Rainbow Dash
  • Fluttershy
  • Rarity
  • Applejack
  • Pinkie Pie (sans Rule of Funny)

This is my logic for the above order. Feel free to comment/discuss:

  • The Elements are canonically the most powerful force in Equestria. They trump literally anything, despite the fact that there are somewhat strict requirements to using them.
  • The Power of Love comes next, as of the Royal Wedding. Chrysalis (the Changeling queen) is able to trump Celestia with siphoned love, and at the end Cadance's love was capable of overpowering the entirety of the Changeling hordes. It's as yet uncertain whether Love would trump the Elements, but I rank them lower because the Elements are more reliable, being as they are physical artifacts that can be gathered by the Mane 6 at any time, while Love is almost useless to anyone except Cadance and relies heavily on Rule of Drama for effect.
  • Discord comes next. It's implied that he could easily overpower Celestia without the Elements on her side. He pretty much toys with the entire cast until the Elements come into play. At the moment, I would be willing to bet that The Power of Love would trump him, being almost equal with the Elements.
  • Nightmare Moon is also capable of overpowering Celestia. However, I rank her lower than Discord because, well, Discord is the embodiment of Chaos, while NM is a corruption of Luna.
  • Celestia comes next, naturally, followed by Luna. As the younger of the two, I estimate Luna to be less powerful; additionally, Nightmare Moon was only able to overpower Celestia because she received a power boost from whatever being corrupted her, thus implying that Luna was weaker to begin with. Cadance follows her two aunts/great-aunts/whatever, as she's far less powerful than them without The Power of Love.
    • Placing one of the Ruling Sisters above the other is kind of dodgy. How much older Celestia is, and whether that means anything is unknown. The only time that they competed against each other, both were augmenting their power. The extent to which the Nightmare Moon state increased Luna power, if at all, was never made clear.
    • Cadance really shouldn't be up with Celestia and Luna. Regardless of whether one believes that Celestia and Luna are especially powerful winged unicorns or that it takes time to reach that level of power, Cadance never displayed power above that of the average unicorn. She was defeated offscreen by Queen Chrysalis, was unable to even try to escape without Twilight's help, and Twilight did most of the work while they were escaping. She did use the Power of Love to help Shining Armor cast out the changelings, but Shining Armor is crazy powerful on his own, so that wasn't a solo showing. Outside of the very rare situations where somepony can be revitalized by the power of love, she should probably be down with the mane five, or in the swing tier with Spike.
  • Twilight Sparkle's magical potential has been commented on repeatedly. I rank her higher than her brother because her special talent is Magic, and you can't get much broader than that, while Shining Armour's talent is supposedly defense or some such. Her brother is still the most powerful unicorn after his sister, however.
    • Suggest placing "normal"note  Queen Chrysalis here. She defeated Cadance without trouble, but used subterfuge to subvert Shining Armor instead of capturing him outright.
  • Rainbow Dash's Rainboom has serious destructive potential, making her far more powerful than the other Mane 6. After her comes Fluttershy, who can easily keep pace when angry or upset. Rarity outclasses Applejack and Pinkie Pie on the basis of having magic, and Applejack has repeatedly demonstrated her physical aptitude. Pinkie comes last, but with a qualification; when Rule of Funny is in play, she demonstrates Reality Warper potential, and in this state could probably outclass the rest of the cast.
    • Fluttershy usually only keeps up with Rainbow Dash when Dash wants her to. Fluttershy did manage to fly faster than Rainbow dash while under extreme duress, with extreme effort, and for a short period of time, but that was when Rainbow Dash was in an altered mental state, which likely had a detrimental effect on her abilities. She also has the stare, but she can't really use that on command. Fluttershy's lack of aggressiveness, combined with her inability or unwillingness to use her abilities on command makes her the weakest of the five under most circumstances. Rarity does have magic, but it is limited in scope and power, and she prefers to use her hooves in a serious fight, though she is a strong fighter like that. Applejack is, well, the jack, and is capable in a wide variety of situations with a number of athletic skills. Pinkie Pie, even without the Rule of Funny, is still very fast and agile, but more importantly, has access to and skill with a number of useful machines that she might have built herself. Finally, she has Pinkie Sense, which doesn't isn't just for laughs.
      • Suggested Mane Five ordernote  Rainbow Dash, Applejack/Raritynote , Pinkie Pienote , Fluttershy.
      • Rarity does make an impressive show of magical prowess when everyone's cutie marks were switched around, seeming to succeed at what she was trying to do with weather control, her problem being that that's not what she was supposed to be doing.
  • Swing Tier: This tier is for characters that switch massively between power levels. Spike fits here, as he usually has below average physical abilities and a weak Breath Weapon, with only his natural armor to balance it out,note  but under the right circumstances can become an adult, shooting him up to around Rainbow Dash or even Shining Armor's level.
    • Cadance would fit well here, due to the situational utility of her only strong ability. Chrysalis would also be a good fit, due to her explicitly variable power level.

After that, it's pretty much fair game.

The Friendship Is Magic's universe's God is making sure that the main six ponies stay close.
It's been shown that Rainbow Dash pulling off a Sonic Rainboom caused the other five to get their cutie marks. I bet that the My Little Pony: Friendship Is Magic universe's God is keeping them snug and close so it has an Ace when things skew to a sour side.
  • Yes, her name is Celestia.
    • My views of Princess Celestia's interactions with the mane cast have always been tinted with the idea that she sees them at least partly as the Elements of Harmony. Rewatch the end of "Fall Weather Friends" with that view. Why would Celestia go to Ponyville to see the falling leaves, when she can do the same thing in Canterlot? Because Honesty and Loyalty are risking a falling out, making the Elements weaker.
    • I thought her name was Lauren Faust.
  • It's some unknown entity above Celestia, Luna, and even Discord.
    • It's HARMONY.

The universe uses a virtue system like Exalted.
Tying in to the guesses about Elements of Harmony having inherent flaws to them as well, it could also be that having an element renders you vulnerable to an Exalted-style Limit Break. Instead of Exalted's four virtues (Compassion, Conviction, Temperance, and Valor), this universe uses six (Friendship, Honesty, Kindness, Generosity, Laughter, and Loyalty), each with their own Virtue Flaws and Limit Breaks. Naturally, a pony that embodies an element/virtue would have the most dots in it possible, leading to some truly spectacular Limit Breaks. Just for fun, let's look at what each of the Mane Six's Elements and possible Limit Breaks could be...

Pony magic forms a field around each pony and has similar properties to electricity.
Specifically, they both are strongest on angled surface. Long pointy things are used as lightning rods, because the electric energy on any surface is the strongest wherever the sharpest angle is. The sharpest angle on a unicorn would be its horn, and because it is so close to their brain, the energy interacts with their brainwaves, allowing to control it directly. The sharpest angle on a pegasus is its wings, and because of this, the majority of their magical abilities come from their wings.
  • And on all ponies, the magical field around them allows them to manipulate any object they can physically touch. At the Grand Gala, we see the pianist pony play the piano, without using fingers. During the parasprite infestation, Pinkie is able to play an accordion without actually touching the keys. And on numerous occasions, we've seen ponies pick things up using only a single hoof.
  • So, ponies have tactile telekinesis? That...would actually make sense, especially when having the regular version is canonically already part of the unicorns' hat.

Earth pony magic manifests as a sixth sense, which is related to their special talent.
It's been confirmed that earth ponies have a magical connection to the land, i.e. Sweet Apple Acres grows better when run by earth ponies. The reason for this is because all earth ponies have the innate ability to simply know how to use their talent best. For example, with her special talent being apple farming, Applejack's "earth sense" tells her precisely when her apples are ready to be harvested. It also tells her how to buck each apple tree so that the majority of the fruit falls into her baskets.
  • Taking the above into account, this can be used to explain Pinkie Pie's "Pinkie sense". Remember, her special talent is making others happy. Most of her various twitches tell her of some sort of danger in the immediate future, and it's awfully hard for someone to be happy when they are hurt. The fact that her "earth sense" manifests as physical twitches is because, well, she's Pinkie Pie.

The Hatching Dragon Test is meant to be an Unwinnable Training Simulation.
Fluttershy's initial reaction shows that baby dragons are probably extremely rare. We don't see a single baby or adolescent dragon elsewhere. My conclusion is that hatching the dragon is designed to be an impossible test for a young unicorn. To see how they will react to not having enough magical power when under extreme stress. This would be a test to judge the character of talented unicorn and help ensure Equestria doesn't have any evil wizards. Twilight's Sonic Rainboom-induced magical seizure might have been the first time in millennia that the test was successfully completed.
  • Taking it further, Spike's egg was a fake, meaning Twilight hatching it was an Achievement In Ignorance.
  • Indirectly supported through "The Secret of My Excess": knowledge on dragon growth and their greed is not well known (Twilight can't find it in books, and neither a pony doctor or a vet know about dragon biology, so she's forced to a more obscure fountain of information, Zecora), suggesting that knowledge of dragons is limited due to their rareness and/or longevity. If Celestia was handing out baby dragons for every student that passed through her school for the last thousand years a dragon, you'd think this would have been well covered by then. Twilight's performance was beyond unexpected.
  • Also supported by "Dragon Quest": the teenage dragons act like a dragon raised by ponies is a strange, perhaps singular circumstance.
  • Supported by Word of God: According to Faust, she used the test for specific fillies that she thought had unique magical abilities, and one which Twilight actually passed. Celestia would go on to raise and train Spike while Twilight continued in school, eventually giving Spike to her as her assistant.
    • In "Dragon Quest", Twilight told Spike that he had been given to her as an egg, suggesting that Spike had been with her ever since. There's no evidence in the show that Spike was raised by Celestia.
      • Suggesting no such thing. He could have been given to her as an egg, then taken away. You're grasping for straws.
      • Perhaps Celestia did most of the actual work when it came to raising Spike, with Twilight playing with him and 'helping', like a child with their first pet.

In addition to the above, the Hatching Dragon test was meant to reveal the suitable Element of Magic.
Anypony who possessed enough power to actually succeed at it would be taken by Celestia as her personal student, and on eve of the fateful day would be sent to Ponyville to make some friends…

The cloud-walking spell from "Sonic Rainboom" never wore off.
The flight spell was mentioned to only last for three days, but the cloud-walking spell wasn't even stated to be temporary. For all we know, Twilight Sparkle, Applejack and Pinkie Pie can still walk on clouds.
  • Pinkie Pie still needed the balloon to sing her invitation to Rainbow Dash for Gummy's birthday. But that episode does not give hints of continuity, so it could go either way.
    • Pinkie would've needed the balloon (or some other flight method) just to get to Dash's place.

Friendship is magic… similar to how Madoka verse emotions are magic.
Cutie Mark = Soul Gem, Cutie Mark Failure Syndrome is the transformation from Soul Gem to Grief Seed, and Nightmare Moon is Luna’s witch form. The ‘outside influence’ in that instance was Kyuubi, and Twilight and co are the Madoka’s of their universe. They didn’t get rid of the system, they used Twilight’s revelation/wish that Friendship IS Magic to focused the contract entirely upon the Elements of Harmony, creating Cutie Mark Shaped Soul Gems they can draw power from/subsequently channel power into.These ponies are saving the universe, one lesson at a time.

The three pony types each have their own kind of magic, but they aren't exclusive to that pony type.
Earth pony magic, unicorn magic and pegasus magic all exist. Unicorn magic is what lets unicorns cast spells, earth pony magic is what lets earth ponies work with animals and plants, and pegasus magic is what lets pegasi fly and perform special effects. Usually this magic occurs most strongly in the associated pony type, but not exclusively. Rainbow Dash has plenty of pegasus magic, letting her fly really quickly and perform lots of special tricks like the Sonic Rainboom and the Atomic Rainnuke, but very little earth pony or unicorn magic. Fluttershy, on the other hand, has a moderate amount of pegasus magic, letting her fly but not terribly well, but she has quite a bit of earth pony magic too, giving her her bond with animals. Applejack has a huge supply of earth pony magic but almost no pegasus or unicorn magic, making her physically very powerful and successful at her work, but she's the only character with no real special powers. Pinkie Pie has some earth pony magic, and a certain amount of unicorn magic, which powers her Pinkie Sense (and other things, depending on how you interpret her abuses of Cartoon Physics). Without a horn, she can't actually cast spells, so her unicorn magic manifests as strange supernatural powers that aren't really under her control.

Friendship isn't just nice, it's SURVIVAL
Not only has it saved Equestria twice, but being nasty, non-empathetic, or antisocial can cause everypony to be frozen into starvation or worse! The ponies brace each other up and remind each other about this regularly, and now we know why Celestia assigned her best student, Twilight Sparkle, to study it.

Earth Ponies can't make an agricultural surplus without Pegasi weather control.
Although they think they can, and the ancient Pegasi and Unicorn leaders also thought that their races couldmanage to make one without Other Pony Races assistance.

Celestia and Luna don't move the heavens unaided.
Instead, they are actually channelling the powers of all the unicorns.
  • Jossed as of The Journal of the Two Sisters.

Unicorn Magic, Earth Pony Magic and possibly Pegasi Magic all work under different principles.
As off "Family Appreciation Day", Earth Pony Magic appears to work with the principles that things need to be influenced in such a way to produce the desired results. Especially when working with a magical crop like Zap Apples. This seems to work similar to Discworld's Witch Magic. It's also been repeatedly shown that Unicorn Magic works by cause and effect, and it seems to be studied in the same way that quantum physics would be studied. This is similar to Discworld's Wizard Magic. Not really sure how Pegasi Magic might work since we haven't really seen enough of how Pegasi society is run aside from weather control and cloud walking.

Also it seems that you don't need to be a certain breed to practice that breed's magic. Fluttershy appears to have the same sort of abilties that Earth Ponies might have (Influencing animals to do what she wants them to do, The Stare etc.) Perhaps it all depends on the correct mindset.

  • Pegasus Magic probably makes it so that everything they build/create doesn't dissipate/fall through the clouds.
    • We know "WHAT" it does, what isn't known is "HOW" they do it. Is it different from the other two methods of pony magic?
    • Seems to work based on physical movement and effort. Weather control, from what we've seen, is based purely on physical ability and skill.

Many of the steps in the Zap Apple Jam ritual are unnecessary.
The Zap Apple Jam ritual is cargo cult science at its best. Granny Smith obviously doesn't understand why it works, only that it does. Its various steps include: (a) Steps that were never necessary, but Granny Smith wasn't willing to risk removing them, (b) Steps that were once necessary but which aren't anymore, (c) Steps which Granny Smith made up to obfuscate the process and keep her family's monopoly secure, (d) Steps which Granny Smith made up specifically to troll the youngsters of Ponyville, and (e) Steps which are actually necessary. She may not even remember which ones she made up anymore. I'm pretty sure the bit with the bunny suits is just to mess with the kids.
  • Alternately, it could all be absolutely necessary, as a form of sympathetic magic. You perform one small act, and it affects the entire crop. Performing multiple of these things increases the crop, and they all affect it. Sure, Granny Smith doesn't NEED to get all the kids to hop around in bunny suits, but it still helps the zap apples grow in a way that only Earth ponies can really understand.

The most powerful forms of magic in Equestria manifest rainbow light.
The Elements of Harmony, the Sonic Rainboom, The Zap Apples... not to mention the use of rainbow in a powerful Love Potion. To ponies, a rainbow kaleidoscope of color could symbolize pure harmonious power: since each pony has their own color pallete, and unicorn magic is color-coded, a rainbow could combine the strengths of all ponies.
  • If what's going on in S4 is any indication, this WMG seems pretty much confirmed. Rarity's suspected Key to the Box of Harmony is rainbow-coloured, and in another scene, rainbow-coloured light played a key element (haha) in getting Rarity to go back and try to set things right with her friends.

Using magic burns calories.
This is probably how all the ponies are capable of eating such huge amounts of sweets and sugary treats without significant weight gain.
  • That certainly explains why unicorns aren't all severely overweight; they seem to do the least amount of work physically. Pegasi and Earth Ponies are both extremely active races (most pegasi control the weather, thus fly a lot, thus are in movement, thus burn calories), and most Earth Ponies work on farms of some shape or form (Pinkie Pie however never seems to sit still so though she doesn't farm, she's still active). It doesn't hurt that ponies usually walk everywhere except to a different town and carriages seem to be more for fun and style than anything, unlike humans who drive cars everywhere.

Everypony and their mother has a connection to an incredible magic power
The Elements of Harmony are just the most understood ones

In Equestria, moving the sun and the moon isn't quite as big a deal as it might seem.
This is a land of magical talking cartoon ponies, after all. A sufficiently powerful non-winged unicorn wizard (especially one with a suitably related cutie mark) could in principle learn how to do it; what makes Celestia and Luna in particular uniquely suited to the task isn't so much raw power as their extended lifespan, which circumvents the need to find and train a new pony for such an important job every few decades or so.
  • "Hearth's Warming Eve" explicitly states that maintaining the diurnal cycle used to be the unicorns' collective job in the time before Celestia and Luna.
Magic fights don't tend to last long, because ponies are glass cannons.
Horn-blasts are really powerful so, essentially, whoever hits first wins. This would explain why Twilight Sparkle is capable of defeating a Changeling with a single blast, why Celestia's duel with Chrysalis was so short, and why the Royal Guard went down so quickly against the Changelings.

Ponies have autonomic magically diegetic projections that they and other ponies don't perceive as being external.
This is how Pinkie and Spike but not Discord or anypony else could see the greyness during The Return of Harmony, and how spike can do things like pop Twilight's daydream in Lesson Zero with his claw, and how Pinkie can do... most of her fourth wall stuff. Spike isn't subject to the Perception Filter, being a dragon and not a pony or a pony-headed Draconequus, and while Pinkie normally is subject to it, she can also see what the audience sees so the perception filter isn't 100% effective on her.

Magic is less effective against resisting or hostile lifeforms.
Twilight is able to lift a rampaging Ursa Minor after she calmed it down and later could stop an entire dam from bursting, but she couldn't (or didn't even try) against the Hydra, the teenage dragons, and even the Cutie Mark Crusaders when they were fighting over her doll. Perhaps it's because magic is less effective against those who actively don't want to be affected. It's why she was eventually overwhelmed by the changelings, trying to blast so many actively hostile creatures tapped her out faster than if they were mere rocks.
  • Of course. Resisting targets get to roll the applicable save.

Earth pony farmers can "talk" to trees with their innate magic and have the trees listen.
They can ask the tree to make sure that when they buck it, the tree's loose fruit falls into two or three small, basket-sized circles instead of all over the ground around the tree. It's been happening for so long that they don't even need to officially ask any more, but the question is now practically implied. Similarly, the ponies have trained the trees to give up on some of their fruits and put effort into other fruits, like how a gardener might trim away some of a plant's fruit to allow its remaining fruit to flourish; this is why there are good apples and bad apples when Granny Smith and the Super Speedy Cider Squeezy 6000 are sorting apples for cider, but no "okay, but not good enough" apples.

It is seen as perfectly okay to time travel or change what kind of pony you are.
We have seen both confusing changes in technology/events which varies often as well as identical ponies that are just another type. I belive that the ponies are not interested in any sort of regulation and just accept changes to the time-stream/species of neighbors as an everyday occurrence. Most ponies just accept things as they are anyway.

The Mirror Pool does not create genuine clones.
It merely creates limited physical-psychological simulacra. With each use by a clone, it has a more limited template to work with. Over time, the physical appearance of the simulacra would have started to deteriorate or exaggerate some feature, too.

It's even in the name; a mirror cannot give a perfect reflection due to the fact that some light always gets absorbed, only in this case the Mirror Pool absorbs a few personal traits.

The Mirror Pool clones are really shapeshifters.
When Twilight zaps them, they don't cease to exist. It looks like they get sent back to the Mirror Pool as pink streamers. This suggests that they continue to exist in some form, which further suggests that they existed before they took Pinkie's form. The Mirror Pool doesn't create clones, it just gives shape and purpose to the shapeshifters that live within.

The Mirror Pool was created by the disposal spell.
The spell Twilight used to dispose of the clones was stated to work just as well on the original. It was also basically a perfect body disposal tool, both removing a body and destroying it. What it it was designed to work on normal ponies in the first place? What if the spell simply strips the victim of form and consciousness, but not life, so that when someone comes by the disposal point, the not entirely dead victims can copy their form?

Both of the above. The Mirror Pool was created as a disposal spell for Changelings.
Say a Changling swarm attacked Equestria before, and the ponies were too soft hearted to just destroy them after they defeated them. The mirror pool was originally a prison for them to live in, dreaming away their existences. Their spirits passed on, but by some quirk their bodies didn't, maybe because it was a physical stasis. Now they imprint on any-pony that enters in the pool, taking their form the chant is just something the re-discoverer made up. It also gives them a portion of the originals emotional energy that allows them to leave the pool. The banishment spell is just the original entrapment spell that they used on the changelings.

Skill can allow a unicorn to more efficiently cast a spell
Shining Armor is able to cast a shield spell that completely encompasses Canterlot, but when the shield comes down, at no point does Celestia or Twilight consider bringing up the shield themselves (IIRC, Twilight stated that this was a unique ability of Shining Armor). If he can cast this potent spell, why can't he use magic of a similar tier, to, say, Fry Chrysalis straight up, y'know? Because magic doesn't just work on power. A unicorn who uses their signature spells can more efficiently cast them than an outside observer. Twilight might be able to create a shield spell, but despite her power, she couldn't create a city-wide shield because she isn't sufficiently practiced in that spell to cast it as efficiently as Shining Armor can, and she's not sufficiently powerful to power on through the requirements.

Any unicorn can cast any spell, assuming they have studied sufficiently.
It just doesn't make sense for publicly available spellbooks to be as numerous as they appear to be if ONLY Twilight Sparklenote  can learn the spells, especially if you actually believe the idea that Unicorns' magic has to be related to their talent, as stated Boast Busters.
  • Confirmed? Celestia's school would be near useless if only a few unicorns could actually learn different spells. Rarity has telekinesis(like all unicorns do) her gem finding spell(Shown to be her signature spell) and also seems to have an insta-dress spell, shown in Boast Busters. Trixie, the other unicron we have seen with more than one spell had telekinesis, light shows(which might have been her signature spell) and at least a spell to change colors.
    • Unicorns probably can cast any spell (provided they are powerful enough to), it's just that most unicorns seem disinclined to learn spells outside their talent.

Magic makes everything function... But the unicorns are using it all up.
Magic in the MLP universe acts like energy of all types in real life; It's the stuff that makes wind possible, that generates the heat necessary to melt snow or to evaporate water, and is necessary to carry out a lot of other natural processes. So why is none of this stuff actually happening?

Why is it necessary to clear the snow after "winter" ends or create artificial rain clouds using water drawn from an artificial tornado? Why is so much more toil required just to create conditions amiable to growing food? The answer is that the unicorns draw upon this magical energy to cast their spells, and in doing so are consuming it faster than it can be regenerated, if such regeneration is even possible at all.

So, why don't the other ponies rise up and put a stop to the unicorns? I can think of three reasons. First, the unicorns, through their proxies the alicorns, control the pegasi, which are faster and generally more militaristic than earth ponies and can easily squash any signs of resistance, in exchange for plush floating cities and lots of down time when they aren't acting as enforcers. In a pinch, the unicorns could probably overpower the pegasi by forcing them out of the sky with their magic or at least protecting themselves with a magically-generated barrier. Second, the ruling class (i.e., the unicorns) are able to distract everybody else through a continuous cycle of frivolous events, such as bake-offs or galloping galas. Third, after a while, and by censoring proper magical science and measurement, it's easy to claim that the manual changing of weather and of the seasons is simply the way things are. Nobody remembers the way that things used to be.

The Enchanted Comics don't work quite how Spike believed they do.
They're apparently sold at a comic store, it's highly doubtful they're at all dangerous. It's likely you COULD leave without winning, Spike just didn't realize it or the only other way to leave is to lose completely. The comics are simply magic, supped up roleplaying/virtual reality games.

Magic wings are different depending on the pony they are given to.
Rarity, being quite fashionable, has fragile but beautiful wings like a butterfly's. If the spell was cast on Twilight or Applejack, they would have been more typical pegasus wings; more reliable and stronger. Pinkie would likely have dragonfly wings to zip around with.

The Mane Six are the new source for all magic.
Based on the Season 4 finale and them giving back all the magic in Equestria.

Starlight Glimmer's spell uses the pony's Cutie Mark as a medium to rob them of their special talents.
Trying to reconcile the "a cutie mark doesn't change who you are" and the "losing/changing your cutie mark messes with what makes you special" theories that have both been shown on the show — cutie marks reflect what was already there, so they don't change you, but they can be used as a medium to get to your talent/destiny and be used to change you that way. So Starlight's spell doesn't just change a pony's cutie mark, it sucks out all their individuality along with the mark.

Building on this; a simple glamour spell that changed your mark would not affect you, only high-level magic spells can affect a pony's talents through their cutie mark — like the unfinished Starswirl spell Twilight cast in "Magical Mystery Cure". It didn't simply switch around the pony's marks and elements, it changed their destiny — the cutie marks were just reflecting what they thought their destiny was based on innate knowledge of what their friends did (which is why, for example, Applejack was making dresses instead of running around looking for gems).

Confidence=Power doesn't just apply to flight, but all innate magic.
In "Top Bolt", the idea that the flying abilities of a Pegasus are tied to that Pegasus's confidence is a major plot point, as Sky Stinger's flying ability goes out the window once his confidence is shot. It's further supported by the main difference in personality between Rainbow Dash and Fluttershy; the former is far more confident and is therefore the better flyer by far. We've even seen more evidence for each of them about how true this concept is: In "Sonic Rainboom, Rainbow's flying abilities were hampered by her decreasing confidence, and Fluttershy, while still not nearly on Rainbow's level, has gotten better at flying as she's become more self-assured and confident in herself.

In "The Beginning Of The End", Twilight spends the bulk of the two-parter completely lacking confidence in herself regarding her upcoming role as Equestria's new ruler. When she attempts to free Apple Bloom from Sombra's brainwashing, she fails miserably. Fast forward to the end of the episode, after Discord gives a Rousing Speech, Twilight has enough power to effortlessly swat aside Sombra's attacks. This is a strong hint that Unicorn magic is also tied to that Unicorn's confidence.

We don't have as much evidence for the earth-oriented magic of Earth Ponies being affected the same way(at least not that I can recall), but with one having the confirmed connection and another one strongly implied, assuming three-for-three isn't too much of a stretch.

Magic solves away wonky physics.
In the MLP universe, rainbows are actual matter (with a very spicy flavor), and depending on the mass of whatever substance rainbows are made of, hearing the boom first may actually be reasonable. Magic can explain away just about everything else. Since Twilight needed to cast a cloud-walking spell for unicorns and earth ponies to walk on clouds, it's reasonable to think pegasi have that magic as an innate ability. Rainbow Dash can fly extremely fast and do a Sonic Rainboom because that's her unique talent, so she's probably innately resilient to those extreme forces. Fluttershy being saved by butterflies is probably a consequence of her cloud-walking ability, and Applejack launching Rainbow Dash so far in the sky could similarly be a consequence of her being an earth pony.

    The Elements of Harmony 
The power of the Elements of Harmony are hereditary.
Pinkie's grandmother taught Pinkie at a young age to "Giggle At the Ghosties" as a subtle way of teaching her how to properly wield ancient power of Laughter. No word yet about what the other characters' parents have taught them.
  • Twilight's parents encouraged their daughter to practice magic.
  • Rarity's parents taught her generosity, albeit in what seems to have been a sink-or-swim way that didn't require much generosity on their part (that being to dump Sweetie Belle on her even when it was inconvenient for her). Apart from Granny Apple, Applejack's family seems to be the type of family where all but the youngest generation are all about honesty and loyalty, with the exception of Granny Apple unless you take the certain point of view that, like the introductory episode with the cliff and as exemplified in the zap apples episode, "Honesty" should be interpreted as "Demanding And Receiving Blind Trust" (in which case, Applejack totally learned Honesty from her Granny). I don't know much about Dash or Fluttershy, especially since Friendship is Witchcraft is overshadowing what little I think I knew about Fluttershy's family.

Everypony has a connection to one of the Elements of Harmony.
However, they don't always have a very strong connection to them, thus leaving the ability to wield the Elements to those who do, and who have a strong friendship with the other five strongest wielders. After all, it'd have to be an awfully Contrived Coincidence that all six Elements of Harmony end up living in the same exact town...
  • It's neither contrived nor coincidental: Recall that this universe's God-monarch walks among her people. Is it too farfetched to believe she had set up a Batman Gambit to save her little sister?

Two or more of the Elements of Harmony can be combined to create other good forces.
And these forces can be used to cure the world of other evils. Of course, All of them combined creates the greatest power of them all, but these lesser powers still have their uses.For instance:
  • Kindness + Generosity = Mercy/Forgiveness
  • Honesty + Loyalty = Family
  • Laughter + Magic = Joy
  • Magic + Kindness = Abundance
  • Generosity + Honesty = Guidance
  • Laughter + Generosity = Playfulness
  • That's actually brilliant. Hope we see that in future episodes...

What the Elements of Harmony actually DO.
This is something of a weird thought I had regarding the various Elements of Harmony when they're by themselves, feel free to add your own thoughts/guesses for these:
  • Magic: Grants the wielder extraordinary magical aptitude, obviously.
  • Honesty: Makes the wielder impossible to deceive or trick, possibly even through magical means.
    • Granted Applejack was tricked by Discord, but then again Discord's effects around Sweet Apple Acres near the start of episode one of the two-parter shrugged off Twilight's Failsafe spell.
    • Problem is, Applejack was tricked by Chrysalis when Twilight wasn't.
      • How about this: rather than Honesty giving Applejack the ability to see through lies, it actually makes other people instantly trust her. Think about it — Twilight took quite a leap of faith in the pilot episode when Applejack told her to let go and fall off of the cliff; In Applebuck Season, everypony asks Applejack to help them out — and we can assume that they all knew about Applebuck Season and that Big Mac was injured, (It's a small town, after all) so they know she's already overworked; In The Last Roundup, Cherry Jubilee hires Applejack rather quickly, and Jubilee even gives her a room in her house. Everypony trusts Applejack, because the Element of Honesty gave her a kind of trustworthy aura.
  • Kindness: Grants the wielder a sort of empathy with Nature, giving them a general understanding of how ponies and other animals work and letting them communicate. This may not work if done for selfish reasons, since you can't exactly be kind if you're selfish.
  • Generosity: Allows the wielder to find and/or make things easier; as you can't give gifts without either finding or making them first.
  • Laughter: May allow the wielder to awaken the soul of a person; bringing joy to those who may have trouble finding it themselves.
  • Loyalty: May give a general increase to the wielder's physical skills, allowing them to be there for their friends, no matter what.
    • Note that Rainbow Dash particularly excels in speed; all the better to rush to her friends' aid.
    • Actually, I think it's more likely increased charisma.

I realize that I'm reaching for some of these, but these are just first draft ideas.

Anypony is an Element of Harmony.
All it requires is for the pony to have a personality that fits one of the elements. However it requires very specific circumstances to use, as the pilot showed. The point is that the mane cast is not some form of Chosen Ponies, the entire gang could be replaced by entirely different ponies as long as there was somepony there to represent each of the specific elements.
  • With one more caveat that they have to be good friends. Since it's an established part of series cosmology that "friendship" and "magic" are synonyms, naturally the pony who gets the fancy tiara is going to have to have a fairly good relationship with the other five, and they with each other. You can't just throw any random sextet of thematically-qualified ponies together and get an Orbital Friendship Cannon.
The Elements of Harmony work by returning things to their proper state.
As observed, the elements restored Nightmare Moon, turning her back into Luna. Used the first time against Discord, the harmony rainbow restored Ponyville to normal (and on a smaller scale restored a circle of grass around the bearers' feet, first.) When used a second time on Discord, they changed him back from a statue. The reason they turned him to stone the first time was because that was the only way to restore the balance between chaos and order. And since Twilight was essentially a nascent Alicorn, they weren't changing her, they were revealing her proper form.
The Elements Of Harmony are incapable of killing.
They've been used four known times to defeat a major threat. All four times, the effects were non-lethal. First two and the last time, it merely neutralized the threat by imprisoning it, despite the fact Celestia and Luna clearly wanted to be rid of Discord once and for all. As the Elements Of Harmony representing the Power of Friendship, they can't be used to kill.

The Elements of Harmony one thousand years ago…
First of all, Celestia and Luna weren't the only users of the elements, there were six, just like the mane six. But The Corruption that made Luna into Nightmare Moon also corrupted the other 4 representatives, Celestia being the only one able to resist. Each one shared the leadership of all equestri until The Corruption appeared. Luna was able to resist it long enough to help her sister to seal their friends. The previous generation could have been:
  • Celestia = Magic: being this one the stronger of the elements, she was able to resist The Corruption, and use the elements.
  • Luna = Loyalty: her love and devotion for Celestia, made her ablo to resist it until the bitter end. later becoming the opposite of her element and the last one to be sealed.
  • Discord = Laughter: He said Pinkie's element was his favorite, and seems to have put special effort in her Mind Rape. He could have Mind Raped Luna before having been sealed.
  • A Dragon = Generosity: he could have been somekind of "Dragon King" and the one who made the theorized "Dragon egg's deal" with the princesses.
  • A Griffon = Kindness: he/she could have, like Fluttershy, been able to talk with animals and helped to bring friendship with all species in equestria.
  • Ursa Major = Honesty: first, a humongous eldritch Mama Bear made out of stars is not prone to trickery, and second, the Ursa stars are used for navigation in our world.
    • I'm a fan of the notion the original Elements of Harmony were the gods of the other races, but they fell apart after Luna's betrayal.
    • Alternatively, the wielders were all winged unicorns. Celestia was the element of kindness, because it would be ironic for someone like Fluttershy to become the supreme ruler of Equestria. Luna possessed the element of loyalty but ended up betraying her own sister. Discord had the element of laughter but eventually turned into a mockery of nature and society. Chrysalis represented the element of honesty until a love poison made her the mother of a deceptive race. Only two more to go.
      • Star Swirl was the Element of magic and an Alicorn in disguise. Since he seems to be a greatly respected figure in the study of magic, and Luna said she knew him. He is just hiding.
    • I am planning a fanfiction about this, except in my version Luna is kindness-see how kind she is in Luna Eclipsed? Anyway, Chrysalis and the Windigoes all form an anti-Elements of Harmony-the Elements of Discord. The four remaining Elements have to be freed by the Mane Six plus Spike because they are all trapped-the Generosity one needs to horde tons of gems in the mines, the loyalty one is paranoid and backstabs everyone, the laughter one is angry at everypony and the honesty one lies about everything and causes chaos in the group. Meanwhile, Chrysalis frees Discord, places the Alicorn Amulet back on Trixie and ressurects Sombra before corrupting Luna and the other four Elements of Harmony again. Keep posted.

The Elements of Harmony are, to some extent, Magic Feathers.
Consider what Celestia says to Twilight at the end of "Elements of Harmony": "I knew you could do it... I saw the signs of Nightmare Moon's return, and I knew it was you who had the magic inside to defeat her, but you could not unleash it until you let true friendship into your heart [emphasis added]". In other words, the magic that defeated Nightmare Moon, and Discord as well, came from inside Twilight Sparkle. After all, there are presumably other groups of close friends among the ponies of Equestria, and presumably others who embody the virtues of honesty, loyalty, generosity, kindness, and laughter. Those are not unique traits. And if all that was needed was a close group of friends to activate the Elements, well, Twilight, as of the beginning of "Mare in the Moon", is the last pony you would send: she has no friends, and shows no sign of wanting any friends. The one thing Twilight had was incredibly powerful magic. She needed to make friends so that she could unleash that magic. Finally, consider the fact that the elements did seem to have been destroyed, only to take on new forms to suit the new bearers, and that the sixth element just appeared for Twilight: those are simply the form that the magic takes, not the substance.

The jewelry referred to as the Elements of Harmony are just a Magic Feather
Their only power is as a psychological crutch to make the actual elements easier to use for the ponies who embody them. They are, in fact, mere projections of the actual elements, which is how they reformed in the pilot. Discord never actually stole them or relocated them, he just made the magic feathers disappear, and then let them reform once he felt the situation was perfect to break Twilight.
  • Alternatively, what Discord was actually doing was suppressing the Elements, which is why he was so incredibly confident; the jewelry he let Twilight find was really fakes after he destroyed the old ones. When she revived their Friendship it broke the suppression, and gave the fake jewelry the same "glow when element is used" effect due to that being what they were expecting to happen.

Elements of Discord/Chaos will be simple opposites of Elements of Harmony
Kindess vs. Malice, Generosity vs. Avarice, Loyalty vs. Betrayal, Honesty vs. Deceitfulness/Deception, Laughter vs. Despair/Gloom, and Magic/Friendship vs. Oblivion/Isolation. Alternatively, Magic will be a common element with Twilight Sparkle ending up on a precipice between them as part of an ongoing seasonal plot/undercurrent (provided another skilled magic user doesn't show up, or they don't just use Trixie).

Conversely, the Elements of Discord will instead be corruptions of the Elements of Harmony.
Loyalty being twisted into slavish devotion, Generosity being twisted into self-destructiveness, Kindness being twisted into obsession, Honesty being twisted into utter tactlessness (to the point of either revealing secrets or insulting the target), Laughter being twisted into mockery, and Magic/Friendship being twisted into darkness/toadyism.

The Elements of Discord will be the following...
There have been many WMG theories that there would be the "Elements of Discord" that would oppose the Elements of Harmony, and Word of God confirms that a villain named Discord would appear in season 2. My theory is that past "bad guys" of the series will be given these elements. After Discord is defeated by the Mane cast, he decides to recruit others to defeat them and counter their Elements of Harmony. The Diamond Dog(s) will be the element of Greed, since they were willing to hurt others to get their diamonds. Gilda will be the element of Betrayal, since she was so quick to abandon Rainbow Dash for shallow reasons. Trixie will be the leader, using the element of Dark Magic. Diamond Tiara will be the element of cruelty (opposite of kindness) since she lacks compassion and respect. Two other ponies will be introduced who will follow the elements of Gloom and Dishonesty. However, by the end of the second season the Mane cast will purge them of the dark magic that took ahold of them and they will become good guys.

The heart-shaped beacon in Hearth's Warming Eve acts as a core to the Elements of Harmony
Much the same way the Master Emerald is the core of the Chaos Emeralds. The only way to permanently destroy/depower the Elements of Harmony would be to somehow extinguish its flame. This is not an easy task, since there would be a lot of friendship and harmony to destroy.

The Elements of Harmony are simply Equestria's weapon of last resort against supernatural threats. Despite their fancy name, they actually have no other powers.
Consider: We never actually see or hear of them being put to non-combat use. Between the fights against Nightmare Moon and Discord in the show, Princess Celestia clearly just kept them in a box in her palace. And before the start of the series, they've apparently been sitting undisturbed in those old ruins for quite some time. Even assuming for argument's sake that Celestia lost the ability to use them herself right after banishing her sister to the moon, she could have readily assembled a group of trustworthy, qualified ponies to do it for her far earlier. So why didn't she...unless, of course, there's no real use for the Elements in times of peace?
  • Maybe only a certain few ponies have the power to use them, like benders in Avatar: The Last Airbender?
    • Celestia has, in principle, the entire pony population of Equestria to draw upon at any time. For her to be chronically unable to put a team of Element bearers together, suitable candidates would have to be extremely rare (even relative to benders, which are actually not that uncommon in the Avatar world), probably to the point that less than six would have to be born within each generation...which would then beg the question why the Elements don't see more use now that the opportunity exists for once. So that's probably not it, or at least not the only reason.
      • Possibly only the Magic element is rare.
      • That's actually the reason given in canon. In order for the Element of Magic to unlock, there must be harmony between its would-be bearer and that of each of the other five Elements. It's rare because this information is NOT stated in any records pertaining to the Elements of Harmony. That's something the pony trying to unlock them needs to learn and understand on their own.
  • Maybe the elements are Cast from Hit Points.
  • If the elements really are only a weapon and nothing else, the decision to not even seek out potential wielders until their need was imminent makes a bit more sense. I mean, would you really expect any group of six ponies of pure enough heart to activate the elements to have no objections to their ruler taking pains to obtain a superweapon, during peacetime, without being able to name any specific need? For that matter if you don't take a cynical view of her character it's hard to even imagine the princess being comfortable with that. This does mean she cut it a little close with actually finding the bearers before Nightmare Moon returned, but maybe she lost track of the date—she did send Twilight off on a quest to make friends as soon as Twilight pointed out that her return was going to happen this year. A thousand years is a long time and that'd be a painful anniversary to celebrate.

Equestria’s most powerful races and the Elements of Disharmony.
Alicorns: Betrayal.
Dragons: Cupidity.
Draconequi: Mockery.
Windigos: Malice.
Changelings: Deception.
????????: ????????.
They must be saving the best (or, you know, worst) for last.
  • Hatred? Dispassion? Ooh, I like dispassion. My Little Industrial Pony: Dispassion Is Science.

There are as many as 18 Elements of Harmony (6 Primary, 6 Secondary, 6 Tertiary) who have their own Bearers and just as many Elements of Discord who have their own Bearers.
The Elements of Harmony and their Bearers, in order of Primary, Secondary, and Tertiary Elements, are:(Primary)
  • Honesty (Applejack)
  • Loyalty (Rainbow Dash)
  • Kindness (Fluttershy)
  • Generosity (Rarity)
  • Laughter (Pinkie Pie)
  • Magic (Twilight Sparkle)
  • Hope (Ms. Cup Cake)
  • Love (Princess Cadance)
  • Courage (Pipsqueak)
  • Forgiveness (Mr.Carrot Cake)
  • Tolerance (Shining Armor)
  • Light (Potential Takanuva analogue named Diurnum)
(Tertiary)Meanwhile, the Elements of Discord and their bearers, in order of Primary, Secondary, and Tertiary Elements, are:(Primary)(Secondary)(Tertiary)

The Elements of Harmony are more effective when used by larger groups.
At some point, the entire population of Ponyville, or even Equestria, will have to use the Elements together.

Princess Celestia has compiled a list of back up Element users.
Now that she's seen what a full set of Element users look like, she's been able to look for those traits in other ponies. Should something happen to the Manes, she has identified groups of six all over Equestria that can potentially wield the Elements of Harmony.note 

The Elements of Harmony’s effectiveness vary on how many pony’s wield them
With one pony being the weakest and six ponies, one for each element, being the strongest. This explains why Celestia was only able to send Nightmare Moon to the moon and Celestia and Luna only able to seal Discord; while the Mane Six where able to banish the evil from Luna and, though still sealed, able to defeat Discord soon after regaining their Element’s allegiance.

The Elements of Harmony always, always search for a way to make everything better.
We've seen the Elements used three times. The first was when Celestia used them against Nightmare Moon, and trapped her on the Moon for a thousand years. The second was when the Mane Six used them against Nightmare Moon again, turning her in what looks like a younger version of herself. The third was when the Elements were used against Discord, and turned him back to stone. In all three situations, the consequences of not defeating the villain were dire, with, literally, the fate of the world hanging in the balance. So why didn't the Elements kill either villain? It can't have to do with the show itself, either its setting or its demographic — the Crystal Heart killed Sombra on-screen, the Friendship Heart thing from the Hearth's Warming killed the Windigos. It can't have to do with the intentions of the ones wielding them — Twilight and Co. didn't know that NMM was Luna, and after all Discord put them through, you'd think they'd have a little more imagination than just turning him back to stone again. That plus the fact that it doesn't seem like any of the Mane Six are in control when the Elements are being used makes me think the Elements have a mind of their own.

The Elements will never kill anyone they are used against, not because of the demographic or the wielders, but because they truly are weapons of Harmony. Above all, they want the relationships between ponies to be harmonious, they just put that into effect in... strange ways. NMM's banishment was because the Elements knew that there'd never be harmony as long as she was anything more than a legend. When she returned, the Elements de-aged her back to a time when she didn't resent her sister at all, and depowered her temporarily so that she could take back control gradually, without as many problems.

And Discord? Well, what the Elements did to him makes him even more frightening: he wasn't de-aged, wasn't depowered, he was just turned to a form where he could flat-out not interact with the world around him, although it can react with him. The Elements knew that his only chance at redemption was if he could listen, if he could be convinced. I wouldn't be surprised if Discord, the second time around, can't see or hear or feel at all. The Elements will not kill, but they know what something is a lost cause.

One as-yet unrevealed purpose of the Elements of Harmony is the creation of new alicorns.
Winged unicorns don't come about naturally. But if the Elements are used by the same group of ponies long enough and sufficient harmony exists between the wielders, one day the Elements' power may cause them all to merge into a single new being with their combined powers and abilities. (Since they're the Elements of Harmony and not the Elements of Brainwashing the decision to go ahead with this probably needs to be ultimately voluntary on the involved ponies' part, which is why it will only work for ponies who are already close friends and willing to take that step further.)
  • Essentially jossed by the Season 3 finale. While the Elements' activation played some part in Twilight Sparkle becoming an alicorn, it's not at all clear that they really did anything more than send Twilight on her way to her meeting with Princess Celestia, and in any event no merger of any kind took place.
    • The process used by Twilight was also said to be only used by her, strongly implying that Winged Unicorns usually aren't made, never mind using the Elements.

Celestia and Luna each had use of three of the Elements of Harmony.
Celestia's elements — Laughter, Kindness, Generosity

Luna's elements — Honesty, Loyalty, Magic

It's mentioned in "The Return of Harmony" that Celestia and Luna, and only them, used the Elements against Discord, and that had the same effect as when the Mane 6 used them on the same enemy. However, when Celestia used the Elements against Nightmare Moon, she only managed to imprison her, but when the Mane 6 used them they were able to return her to her regular form. It is my belief that the only reason Celestia was unable to save Luna was because she could not use the elements at their full power and had to force the power out of the Elements she already had.

  • Celestia worked a thousand years to free her sister and Luna's inability to deal with people back them probably meant she didn't have many friends. I'd swap Loyalty and Magic with Generosity and maybe Laughter.
  • Partially confirmed with S 4 E 2: When the two square off against Discord, they are both wearing saddlebags. Celestia takes out the elements of Magic, Kindness, and Generosity from hers, while Luna has Loyalty, Honest, and Laughter.

There is a secondary set of elements known as the Elements of Virtue.
While Harmony may counteract chaos, niether Chaos nor Harmony are absolute good or evil. This means that Harmony can be pushed too far, as well as be used for evil purposes (i.e.-the Borg, Cybermen, ect.). To counter act this, the Elements of Virtue are used to keep the Harmony good and in turn Harmony keep Virtue in balance. The virtues are as follows.

  • Freedom — counterpart to Magic.
  • Justice — counterpart to Generosity
  • Honor — counterpart to Honesty
  • Duty — counterpart to Loyalty
  • Mercy — counterpart to Kindness
  • Hope — counterpart to Laughter

The Elements of Harmony can change their form depending on what species is wielding them.
They took the forms of necklaces and a big crown thingy because that's apparently the best way that a pony could harness their power. But they can take on other forms to suit other species, such as rings, lockets, hats, swords, shoes, gems, wands etc. As long as the individual displays their chosen element, the element can suit whoever is wielding it.

The Elements of Harmony change color depending on who uses them.
If you remember that in the original narration of the show, the six elements are shown as six colors; orange for Honesty, red for Loyalty, green for Generosity, pink for Kindness, blue for Laughter, and purple for Magic. However, in the show Generosity is now purple and Magic is now magenta. The only possible explanation I can think of is that they were those colors when Luna and Celestia used them, but when Rarity and Twilight used them, they just changed to more appropriate colors.

The Elements of Harmony are tied to "Pride".
The majority of the Elements of Harmony seem to be filled with Pride thus it seems that Pride might be the source of the Elements of Harmony. It might turn out that the creator of the Elements is infact a villain who is the embodiment of Pride and thus worse than Nightmare Moon, Discord, Queen Chrysalis or even King Sombra and is infact immune to the Elements of Harmony.

The show's big bads each represent the opposite of an Element of Harmony.
Nightmare Moon — Betrayal (vs Loyalty)
Discord — Chaos (vs Magic)
Chrysalis — Deceit (vs Honesty)
Sombra — Fear (vs Laughter)
Tirek — Greed (vs Generosity)
?????? — Malice (vs Kindness)
  • Starlight Glimmer's plans revolve around what she perceives/presents as a kindness, yet is anything but. -woggs123

The Elements can only be wielded by a certain set of bearers (not necessarily ponies) and still work.
That's why Spike carrying the Element of Loyalty didn't do anything; despite matching it to a T (he puts up with so much from Twilight...) he couldn't help because the Element was bound to Rainbow Dash, and would only work with her.

The giant World-Healing Wave that the Elements generated during (both of?) Discord's reigns...
... wiped everypony's memories clean of what Discord actually did, save for the Element bearers themselves (and former Element bearers like Celestia and Luna). It's pretty logical — the kind of shenanigans that Discord got up to, it's not too unlikely that he might have driven many ponies permanently insane, to the point where hitting "rewind" on their brains was the only way to heal the trauma. It's also a pretty handy explanation for "why aren't the Mane Six worshiped as heroes for kicking Discord's ass?" — aside from Celestia and Luna, no other pony remembers what they were saved from. Sure, they went to the ceremony honoring the Mane Six, and they might have been told later on that "this really bad dude called Discord came along and made things hell for everyone, and then these six brave ponies kicked the crap out of him", but that's still not the same as actually remembering what living under discord was like.

The same may or may not have happened when Celestia and Luna originally sealed Discord up, which may account for the lack of accurate scholarship regarding Discord (Cheerilee simply says that "this statue represents discord", not "this guy once ruled over Equestria and made life miserable for everypony").

The Elements of Harmony as seen in the pilot and the flashbacks in Princess Twilight part 2
are "blanks"The elements as shown in the past are basic gemstones with the exception of Magic. But when the Mane Six receive them they shift to form the dominate shape in their cutie mark again with the exception of Magic which already matches Twilight. At the end of Princess Twilight part 2 The elements are taken away from the Mane Six and given back to the Tree of Harmony but they don't revert to their gemstone shape instead the tree conforms to their new shape. With what follows, the reveal of the lock box with six keys, it would seem the tree acted as a sort of vault protecting the chest. The manner in which to unlock the vault appears to be to attune the five "blank" elements to bearers then return it to the tree.

The Tree of Harmony teleported itself around as a defense mechanism against Discord's plunder seeds.
Okay, this is mainly to address the whole "why didn't the alicorn sisters tell anypony about the Tree of Harmony" and "why didn't the alicorn sisters put the Elements back inside the tree after beating Discord" complaints on the Headscratchers page. But still, it works — Discord mentions that the tree's defenses stood against his seeds for a thousand years, but he never mentioned what those defenses actually were. The tree randomly teleported around the Everfree (and maybe even beyond it) whenever it felt Discord's seeds getting close, but wherever it went, the seeds would follow. The alicorn sisters couldn't find it, and eventually forgot about it/wrote it off. When it was finally beginning to run out of juice, the tree teleported itself back to its original location beneath the sisters' old castle, in one last, desperate gamble that they would show up and return the Elements.

Celestia and Luna using the Elements of Harmony by themselves
Personal theory on Element assignments:

  • Celestia: Magic, Laughter and Loyalty. Celestia is, in her own way, an inveterate prankster — episodes such as The Ticket Master and Lesson Zero show how she's not above using trickery to get a message across, and she's vastly more freewheeling, jovial and informal than her stringent, uptight and protocol-obsessed younger sibling — Laughter is definitely her Element. Loyalty is another strong point of Celestia's — she braved many dangers to defeat Discord out of love for Equestria, and was later forced to choose loyalty to her kingdom over the happiness of herself and her own sister, separating them for a thousand years. Lastly, she's shown to be a creature of immense magical power — capable of taking on her absent sister's duty of moving the Moon in addition to her own duty of moving the Sun, of dispelling runaway spells with a minimum of effort, and let's not forget that Chrysallis seemed very surprised that she mustered enough power to defeat Celestia.
  • Luna: Kindness, Generosity and Honesty. Luna's kindness, although not always obvious, makes itself evident when it's required — notice how in Luna Eclipsed she immediately runs to the aid of Pip when she believes he's in danger of falling into the apple bob tank. Honesty's a harder one, and I'm tempted to assign it to her merely because it doesn't fit with Celestia (who while rarely outright deceptive often doesn't tell the whole truth), but it's quite clear from her interactions with Twilight in the above episode that she's straight-talking and maintains a realistic assessment of her situation, even when self-delusion might make her feel better. It's a bit of a stretch, but Honesty seems like her Element. Lastly, the Element of Generosity strongly fits Luna's personality — in fact, tragically, it's part of the reason she became Nightmare Moon: she made Equestria's night beautiful and yet her charity wasn't appreciated.

The Elements are actually the souls of six long-forgotten ponies who gave their lives to protect their world and the Tree of Harmony, and a little bit about the Mane 6's relation to the Elements.
And each pony who became an Element had a very unique cutie mark that represented the Element they became, as their talents, sans magic, are extremely rare to have as special talents or purposes in life, making them extremely powerful ponies. Many years ago, long before Celestia and the founding of Equestria, there was a great war between the many different type of residents, and the ponies were losing. It was a war dominated by hatred and chaos itself. Destruction was falling all over the land, and things grew worse with each passing day. The land was growing desolate and unusable, the flora more and more unstable, and the fauna, violent and deadly. Out of this terrible war, monsters like Discord and the Nightmare Forces were born. Six ponies, six ponies used as living weapons against the opposing factions, were the only ones who could see how fruitless the fighting was, and sought to find a way to save the world from total destruction. Seeking a non-violent way to end the war, they went to find a magical tree told only in ponytales, a Tree that in the stories spread harmony throughout the land. On finding it and proving their worth to the Tree by saving and defending it, the six gave their lives to the Tree of Harmony to protect their world, and ensure that when needed, they can always be called upon, in exchange for protecting the Tree itself from harm. The animals, weather, and flora were calmed, and the war itself ended as harmony spread throughout the land. The Tree contained what it and the six ponies could not defeat into the trees around the Tree of Harmony itself, which became the Everfree Forest (except for the Nightmare Forces, which were forcibly banished to the Moon, far out of pony reach).

For many years, the Tree and the Elements remained relatively dormant, together in peace and immortality, preserving harmony, until Discord gained power after fleeing his prison deep within the Everfree Forest. When Celestia and Luna came to call, the Tree gladly gave up the Elements so they could now fulfil what they wanted from it; to protect their home. As they could not, or rather would not destroy Discord, they merely turned him to stone, effectively freezing his powers far better than they had been when he was trapped in the Forest. The Elements were stored in the Castle of the Royal Pony Sisters until Luna sought to defeat the Nightmare Forces and lost, becoming Nightmare Moon, and Celestia used them once more, only succeeding in banishing her. For a thousand years, the Elements slept in the abandoned castle, waiting to be needed and to be, one day, reunited with the Tree of Harmony so as to continue protecting the Tree and the land in the best way possible.

The Mane 6 are the closest to being the Elements reincarnated (as close as one can be when there's not a soul to reincarnate), but not exact, as each has a different Cutie Mark (ie, passion/purpose in life) than the Elements themselves when they were still ponies. This is why they can harness the power of the elements better than even Celestia herself could, as they were able to destroy the Nightmare Force possessing Luna, where Celestia could not. They were chosen by the Elements, who greatly saw themselves in these six ponies, aiding them in battle. The Tree of Harmony began to die, no longer able to protect itself without the Elements there to ensure its safety. When they were finally returned after thousands of years apart, their magic was even more superior than it had been before, allowing the Tree and the Elements to destroy the Plunderseeds.

Elements of Harmony for the Pets
  • Tank, who is nice to even the cattiest of cats, has Kindness.
  • Winona, who is always happy and trying to play with others, has Laughter.
  • Gummy, who never fails to speak his mind, is Honesty.note 
  • Aloysius, for always being ready to lend a helping feather, possesses Generosity.
  • Angel, who is always there when Fluttershy needs him despite being a total douchnozzle, is Loyalty.
  • Opalescence, for being a stuck up jerk to her friends, has Magic.
    • Not OP: I don't get the last one.
      • While Opalescence has shown a good grasp of social manners, she and early Twilight could be grade-A jerks to people.
    • I don't know about that, but cats are often associated with magic, being common familiars for witches and such. So one could justify it that way (since magic doesn't have anything to do with rudeness).

The Elements of Harmony do more than just purify or seal evil.
They can show their target who's doing a great evil precisely just why it is so and would bring nothing but pain and suffering. That's the reason why Princess Luna (bringing forth an apocalypse) and Sunset Shimmer (accountable for trespassing, theft of royal property, resisting arrest, one count of dog-(or-dragon-)napping, six counts of attempted murder (one on a princess), multiple cases of enslavement, and property damage) were easily forgiven.

    The Sonic Rainboom 
The Sonic Rainboom is some sort of time-space shift.
It sends them to a seperate alternate universe every time it's used, and it's incredibly risky. Think in The Cutie Mark Chronicles. The first Sonic Rainboom shifts everyone's fates so suddenly and extremely, acting like a in-universe Deus ex Machina. This sent them to the a more idealistic universe. Somewhere out there, there's a Darker and Edgier universe where they all grew up miserable. The second sent them to a nearly-the-same universe, with some slight changes in certain traits explaining, such as the increase in Pinkie's teleportation.
  • I just finished writing a fan fiction on that premise, without having seen this post.

Sonic Rainbooms warp reality.
First off, their very animation implies that they involve breaking a barrier that is not intended to be broken. Thus, the effects of pulling off such a move need to be seriously taken into consideration. They seemed simple at first when it was first seen in "Sonic Rainboom", briefly knocking witnesses out of character such as turning Fluttershy excitable and Rarity humble.

But this takes on a whole new layer of meaning in "Cutie Mark Chronicles". Applejack managed to miss the actual Rainboom and Rarity didn't behold it herself, so they were largely unaffected. Fluttershy was only minorly affected, causing her to remain calm and brave even as the other animals panicked. But then we get to later stories, and we realize that this Rainboom was directly beheld by both Twilight and Pinkie. The results? Twilight suddenly found herself tapping into an immense power she couldn't control, forcing Celestia to take her under her wings to help her. And Pinkie Pie, an otherwise normal earth pony beforehand, became the Cloudcuckoolander and borderline Reality Warper (exceeding the powers of known unicorns and pegasi) that she is today.

We were lucky the first two times. Who knows what could happen if such acts of breaking the rainbow barrier continue unchecked?

  • Alternatively, this is the standard effect of breaking the rainbow barrier... But if too much of it is used, it'll reduce the world to cloying saccharinity, sapping the intellect of all ponies and destroying their individuality in the process. In addition, it will turn at least certain pegasi into earth ponies... Raibow Dash and Scootaloo first and foremost among the afflicted. If the rainbow barrier is breached too carelessly and too often... this may be what Equestria reverts to!
    • It was broken a 3rd time in Lesson Zero, so we may be getting there…

The Sonic Rainboom is magic.
The prismatic wave (the rainbow-colored shock wave) is caused by the sonic pressure wave compressing the ambient magical energy of Equestria along with any magical energies emitted from the entity that obtained supersonic speeds. This compression would cause the magical energies to become temporarily visible and even enter a high intensity state.
The contrail (the stream of rainbow that flows behind) is an after image blur, the long duration of such made possible by the large quantities of exhaust energies shed by the pegasus from the natural thrust vector magic they unconsciously use to obtain supersonic speeds. As such, the contrail is largely harmless though potentially very pretty. The contrail's coloration would be dependent on the coloration of the pegasus.
The high intensity energies within the prismatic wave would have properties similar to Comic Book radiation, namely they would give things exposed to them strange powers and abilities. This probably only effects creatures that already have at least some degree of magic (to help explain why plants and such seem to be unaffected) and any powers or abilities gained would follow along the natural paths of magic for the affected creature (so ponies would gain powers in relation to their special talent.) Let's look at the mane six:
  1. Pinkie Pie is the only one whose story shows that she was caught by the full force of the shockwave, and therefor would have received a maximum dosage of the high intensity energies. Pinkie Pie's special talent is making ponies smile (Parties are just a good way to make large numbers of ponies smile at once). This would be why Pinkie Pie can access Toon Physics, which allows her to perform feats and use abilities that defy explanation by modern unicorn magic, provided they are humorous or make for a good gag.
  2. Fluttershy was in the middle of the forest when the prismatic wave went over head. The trees of the forest might have somehow prevented most of the energy from reaching the ground, causing most of the high-intensity energies to pass overhead, though some might have leaked down to Fluttershy. That would explain her 'Stare,' which certainly is a strange ability and can is generally used to influence animals, linking it to her special talent.
  3. Applejack was in Manehatten at the time and didn't even see the prismatic wave. All she saw was Rainbow Dash's contrail heading in the direction of Ponyville.
  4. Rarity saw the prismatic wave pass overhead, but between her and the origin point of the wave, was the Rock, which would have acted as a windbreak. The gems inside the rock could have absorbed any energies that came in contact with it, increasing the effective size of the wind break effect.
  5. Twilight Sparkle was in Canterlot and seemingly far from the Sonic Rainboom. So her magic would have been unaffected by the prismatic wave, though the loud boom startling she was trying to use her magic (possibly coupled with whatever subtle shifts in Equestria's ambient magical fields the Rainboom would have caused) caused whatever was blocking her from accessing her titanic pools of magical power to break loose.
  6. Rainbow Dash was at the epicenter of the sonic rainboom, though it could be argued that the rainboom started just behind her and propagated at a slower speed than what RD was flying at. As such, Rainbow Dash would have had minimal contact with any high intensity energies.
With Rainbow Dash's Second Rainboom, it can be assumed that whatever spared Rainbow from being affected by the first Sonic Rainboom would be the reason why she, Rarity, and the Wonderbolts were unaffected by the second one. Also the second rainboom was close to the ground and the high intensity energies might not have reached all the way up to Cloudsdale, which is why nopony in the stadium was affected (as far as we know) by the high intensity energies.

Discworld science explains the sonic rainboom.
While only Unicorn Ponies can cast spells, Pegasus Ponies display many supernatural talents of their own, and Earth Ponies have at least their cutie marks as proof of an uncanny nature. But beyond the ponies themselves, all of Equestria appears to be a land of magic.
In this entry, we present evidence that the world of Equestria may in fact obey the conventional laws of physics under a Discworld-like Background Magic Field. An experiment realized by a young Pegasus Pony named Rainbow Dash literally brings new light on the subject.
A recognized property of the Discworld's BMF is that any light passing through it is slowed down until its speed becomes roughly equal to the speed of sound. As a result, any moving object breaking the sound barrier will also break the light barrier. Close and distant observers can then hear a sonic boom and see a prismatic flash, always perceived as if simultaneous with each other.
In the two occasions where Miss Dash created what she calls a "sonic rainboom", all witnesses described the phenomenon in terms remarkably similar to the above paragraph. We think this is solid indication that Equestria's magic may not be unlike the one studied at the Unseen University.
Further investigation at Princess Celestia's School for Gifted Unicorns revealed that the first of those two "sonic rainbooms" may also have caused a thaumic chain reaction within this reputed establishment. We were assured it was contained without any long-term damage.

A sonic rainboom requires the motivation of doing something for the sake of another.
In "Sonic Rainboom", Pinkie Pie says that Rainbow Dash is the only pony ever to have done it (though this can't be literally true, as there are apparently legends), and she'd only done it once before. When? Why, when racing some colts who were bullying Fluttershy about her weak flying! And her second time? Saving the life of Rarity and the Wonderbolts! Training could possibly help a pony with the necessary speed; alone, however, it could never cause a sonic rainboom, nor could trying to show one off. I wonder, if they were to research the legends of the sonic rainboom, they might discover ponies who were just trying to help their friends...

Sonic Rainboom is a powerful, temporal boost for a pegasus' innate magic.
The pagasi magic gives them some mild physics-breaking powers like walking on clouds and flight, but they are still mostly bound by it's laws. Specifically, when a pegasus is trying to fly too fast even by Equestria's loose standards, they are pushed back by reality itself.

However, if a pegasus is determined enough, they can push themselves to break reality's barrier and cause a Sonic Rainboom (it was probably easier for Rainbow Dash, since she's the Element of Loyalty and the reason for both Rainbooms were her friends). At this point, the laws of physics give up and stop restraining the given pegasus. Let's see what kind of laws we've seen abolished:

  • Friction: The rapid gain of speed after a Rainboom is not caused by acceleration — rather, the pegasus is no longer bound by air resistance.
  • Inertia: Rainbow Dash could make impossibly narrow turns not even losing a fraction of her speed.
  • Gravity: The reason why Rainbow Dash was able to carry three Wonderbolts and Rarity and still fly and maneuver at top speed is because weight had no effect on her.

It implies that after performing a Sonic Rainboom a pegasus could possibly do some other interesting things, like going off to space, flying around the world fast enough to make time flow backwards or usurping Celestia as the ultimate ruler of Equestria. However, none of the above occurred to Rainbow Dash at the right time.

Note that because of it's nature, Sonic Rainboom could cause any of the reality-warping effects mentioned in WMGs above.

The speed of sound in Equestria is lower than it is in our world.
Even beyond the existence of magic and tiny pastel ponies, the atmospheric physics of Equestria are rather weird. Clouds are smaller and form at lower altitudes than in the real world, for example. If the speed of sound were much lower — say, about 50 metres per second instead of 340 — then, while breaking the sound barrier would still be very difficult for fluid dynamics reasons, it's much more plausible. At the beginning of Sonic Rainboom, Rainbow Dash spends about twelve seconds diving at a roughly 45° angle at something close to the speed of sound, which would mean diving about four kilometres. It just doesn't feel like she's covering that much distance, if Fluttershy can still see her as anything but a tiny blue speck against the (also blue) sky. If the speed of sound were 50 metres per second, that's 180 km/h, which is the speed of a very fast modern car. I think that's still pretty impressive for a little pony with tiny wings.

The Speed of Light is slower than the Speed of Sound in Equestria.
The Sonic Rainboom in, well, "Sonic Rainboom" didn't seem to cause the same amount of havoc that would have occurred in our world if something the size of a pony broke the sound barrier, but we have no idea what would really happen if the light barrier were broken. Maybe the light barrier causes magic and rainbows to happen in their world instead of the timey-wimey havoc that might happen in ours, but breaking the sound barrier merely does the normal, real sonic boom thing.

A Sonic Rainboom only forms when a highly magical object or creature breaks the sound barrier
.The more powerful the magic, the larger and brighter the shock wave.An inanimate object like a bullet or rocket which broke the sound barrier would create a normal sonic boom, just like in our world.

Sonic Rainbooms make the world a more magical place.
Any time one is created, something, somewhere, becomes better. Whether it's a filly earning a particular cutie mark against all odds, a pony achieving their wildest dreams, a miraculous rescue from certain death, or just a wave of smiles all over Equestria, it is guaranteed to occur, and it will always be special.

The Sonic Rainboom does not break the sound barrier.
Rather it's a burst of water particles drawn from the air and/or clouds caused by a shock wave. Circling the clouds is not just a stunt, but it also has a practical reason. Pegasi Magic includes the ability to manipulate the wind, the clouds and the water in the air.

    The Alicorn Amulet 

  • Grants it's wearer whatever her or his heart most desires, regardless of their race. For example, to pegasi it can give speed beyond measure and for earth ponies, it can grant the might to overpower anything or anypony. As for unicorns, it could help them unlock their inner abilities.
  • A refinement of the previous point: The alicorn amulet is usable by all three pony races, and massively enhances the abilities that are inherent to each race. Since alicorns possess the abilities of all the races, it would make sense for it to be usable by anypony (So a pegasus would gain enormously enhanced flight and weather control, and an earth pony would have Super Strength and possibly some matter of earth/nature control).

The Alicorn Amulet does not corrupt its user.
The Alicorn Amulet doesn't really have any kind of corrupting factor to its magic. However it is generally assumed it does because none of its previous wearers have ever been able to resist the temptation of abusing their newfound power.
  • To further this argument, look at what Trixie does shortly after removing the Amulet: her first act of power is to fire a spell at Rainbow Dash that would make her "writhe in agony". It doesn't work of course, but it does raise the question: if the amulet does indeed have a corruptive influence on the wearer, why didn't Trixie instantly revert back to her old, less psychopathic self as soon as she took it off, rather than long after she realized her powers were diminished? This is further evidence that the corruption is not forced upon the user, but rather comes from the user themselves as a result of too much power.
    • Bearing in mind, of course, that Trixie got decidedly nuttier as time went by. Remember, this is a showmare who travels in a wheeled cart... who decides she "doesn't trust wheels". Some decidedly progressive insanity there, which helps explain why a stage magician didn't pick up on Twilight's use of stage magic.

The Alicorn Amulet is made from stolen unicorn horns.
Yep, that's right, 100% percent real alicorn. The pain and rage of the unicorns whose horns were stolen is still suffusing the amulet, causing whomever wields it to lash out at everyone around them.

The Alicorn Amulet doesn't grant its user knowledge on how to cast spells
It's like a Sa'angreal from Wheel of Time. It grants power and control and allows the user to cast spells at levels they couldn't ordinarily pull off without hurting/killing themselves, but they can't actually cast spells they don't know how to cast. That's why Trixie was goaded into stealing the fake amulet from Twilight. She believed that it could not only grant its user power, but knowledge as well, so an amulet that could pull off spells at her old power level but also endow her with knowledge was too tempting for someone corrupted by the amulet.

Expanding on the above, the Alicorn Amulet is a Sa'angreal made by The Dark One from Wheel of Time
It would explain its power and why it turns people evil.

Amulets don't literally multiply one's power.
When you use an amulet, you use the amulet's casting power instead of your own. If the amulet is substantially more powerful than the caster, then it is effectively multiplying the caster's power, but a more powerful caster that's less powerful than the amulet using the amulet would only be able to pull off spells at the same level as the amulet-powered weaker caster, assuming the same knowledge level.

Amulets function like they do in Dungeons and Dragons
That's why Trixie took the Alicorn Amulet off instead of just doubling up. It's a neck slot item, and you can't equip more than one neck slot item at a time.

The Alicorn Amulet was created to allow non-unicorns to cast spells
As a side effect, it helps unicorns casts spells, allowing them to cast spells with greater power and skill than they could without it.

The Alicorn Amulet is the Equestrian version of Majora's mask
Both got attached to and corrupted those who had been emotionally wronged. Had Twilight not tricked her, Trixie would have become a lifeless puppet and the amulet would have risen to its full power.

The Amulet was created by Discord
A device that causes the user to sow dissent and havoc wherever they go? A device that causes them to develop a distrust of wheels? Sounds like something that he'd do.

The amulet was a failed attempt to create more alicorns.
OK. So the rule seems to be that if a pony overcomes a fairly significant trial, they can become an alicorn. The Alicorn Amulet was a failed attempt to use this rule to mass-produce alicorns. Ponies would be tested for worthiness by given a massive amount of power. They would then have to summon up enough willpower to resist the corruption. The power boost would then become permanent as they ascended to alicorn-hood. Unfortunately, no one has been able to resist the corruption, and so the amulet was declared a dangerous dark artifact.
  • How is that the rule? The only onscreen winged unicorn transformation was the result of a spell and the Elements of Harmony.

    Time Travel 
How Starlight changed the past while Twilight couldn't.
When Twilight used a time spell in It's About Time, the rules of You Already Changed the Past were in full effect. But the time spell used by Starlight in The Cutie Remark seemed to leave the travellers free to change the past however they wanted. Not only did they have Ripple Effect-Proof Memory, they also suffered no physical change from altering their own past. While this seems like a contradiction due to lazy writing, the episode actually gave a clue regarding how it works. In all timelines, the Tree of Harmony remembered the Cutie Map and recreated it. Since Starlight's spell used the Cutie Map, and through it the Tree of Harmony, the spell was similarly able to remember and recreate the travellers, effectively shielding them from the rest of causality. In sci-fi terms, the spell/map/tree acted like a teleporter with a pattern buffer and an internal data time loop.

The "key" changes to the alternate timelines was not the Mane Six's cutie marks
The lack of cutie marks only justifies the existence of one Bad Future. Thetrue "key" to the bad futures were probably the alterations in Cloudsdale-meaning that in the other bad futures, any member of the Mane Six other than Rainbow Dash or Fluttershy wascompletely irrelevant.

The time limitation on the fixed time-loop spell from "It's about time"
The spell could only send Twilight back a week because of the second law of thermodynamics. Travelling back in time in a fixed loop decreases entropy in a system, which violates the second law. However, as some scientists currently believe, it IS possible to TEMPORARILY decrease entropy in a system through some clever science. The spell temporarily decreases entropy, but of course there is a limitation to how far thing can be stretched, and for this spell it's seven days.

     The Cutie Map 


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