Chapter 6 of Moondancer's Misguided Mission reveals us that Sunset Shimmer treated her daughter Sun Shimmer as a weapon to be used against her feudal enemy, House Twilight. This resulted in neglecting Sun's childhood to give her hard training instead.
Alpha Bitch: Wish Shine, Twilight Shine's cousin, is one to every other pony. She also almost killed her cousin's coltfriend when he saw through her disguise in chapter 48 of The Magnificent Six.
Sun Shimmer, the assistant teacher from Mustangia, in Moondancer's Misguided Mission.
Although, it is revealed that her mother Sunset Shimmer made her into one by being a bigger Alpha Bitch than Sun is.
Apple of Discord: Sun Shimmer in Moondancer's Misguided Mission acts like one to the residents of Dream Valley as part of her mother's plan to ruin Twilight Sparkle's descendants.
Artifact of Doom: The Flashstone is the culprit of corrupting Luna to Nightmare Moon and Midnight to Tirek.
Bad Future: The post-Equestria era to those few individuals who have survived from the Equestria era.
The Mane Six of the era are quite offended by this attitude, however. They take particular objection to Applejack's attempt to Set Right What Once Went Wrong, angrily declaring that, even if they're not as perfect as Equestria, they still have the right to exist instead of being replaced by a continuation of the Golden Age.
Balkanize Me: Subverted. What used to be Equestria is now a Confederacy of 5 sub-automous city-states, and several independent small kingdoms.
In Twilight Then, Twilight Now, Tambelon is lost to Grogar and his Troggle army and the Mane Six's coltfriends disappeared with it, but they have delayed an all out war to several centuries and in the present Ponyland, Tirek is Killed Off for Real and the war is won to the ponies.
In Ponyville Generations: Spike's Story, after Ponyville has returned to the outside world and became a normal village again, Spike lived happily with his girlfriend Whimsy for years, until Whimsy got killed by Tirek's Strydon hordes and Spike was captured to be enslaved in Midnight Castle.
In The Magnificent Six, Cadence did a Heroic Sacrifice to destroy the animated Alicorn Amulet like what Celestia and Luna did before her and because of it the Princess Ponies confiscated the Elements of Harmony from the six fillies, but she also ensured that Ponyland will get the heroines it needed.
Break the Cutie: It turns out that Ponyland-era's Applejack's "silly filly" behavior is due to her actually being the Equestria-era Applejack, who has been immortal for a thousand years and steadily traumatised by the increasing decline of ponies. Is it any wonder she is tempted by an offer to Set Right What Once Went Wrong, allowing her to prevent the Fall of Equestria?
Also, the Snowponies (who are descendants to the Crystal Ponies) lost a lot of faith and are hostile towards Cadence, whom they believe had abandoned them at their greatest time of need during the destruction of the Crystal Empire.
Canis Latinicus: In chapter 49 of The Magnificent Six we have a spell, with very fake Latin.
Creation Myth: The first chapter of The chronicles of the Horsemaster is a Creation Myth of the ponies' world in a Horsemasterist belief.
Culture Clash: Being an Equestrian, Cheerilee can't find anything wrong with not wearing a bow on her tail. Moondancer, however, thinks otherwise.
Also involving Cheerilee, in YOU EAT MEAT?!? chapters in My Little Short Stories, she didn't take the knowledge that some ponies are omnivores quite well.
In Honeymoon in Selenia chapters in My Little Short Stories, let's just say that Twilight had a big surprise in culture differences between Dream Valley or the Confederacy and New Equestria (such as whinnying and snorting for language, Alicornism as an official state religion, ponies living in villages instead of citadels and the locals are friendlier and more forgiving than their Dream Valley or Ponyland Confederacy counterparts.
Deal with the Devil: In Moondancer's Misguided Mission, Sun Shimmer admitted in making a pact with the Windigoes to help her freeze Dream Valley while giving them unlimited source of hatred in there. It backfired on her after Moondancer and her friends defeated her and freed whole of Dream Valley from the Windigoes' icy grip.
In Harmony Dies in My Little Short Stories have the queen of Dream Valley at the time, Sky Skimmer, decide to take the offer from Tirek that she will destroy the Tree of Harmony to weaken Equestria so he will invade it while leaving Dream Valley alone, as long as they stay neutral during his invasion.
Demonic Possession: Sombra, Luna and Midnight had this happen to them, mostly due to the Flashstone corrupting them enough to be open to the Tirac (who is the ponies' equivalent to Satan) to possess, turning them to King Sombra, Nightmare Moon and Tirek.
"The gathering darkness clouds in over Equestria, slowly eclipsing the glow of the light of friendship. Since the death of Princess Celestia, our fair land has been plagued by maladies of every sort. More and more townsfolk and small landholders are falling into heavy debt, causing them to fall under the power of the wealthy landholding ponies to whom they indenture themselves to. Inflation is skyrocketing, and mares and stallions who carefully saved their entire lives, now find their hoarded bits suddenly worthless. Greed has eclipsed friendship, as corruption has seeped into every level of society....
....the religion of the great Horsemaster swells in believers, the disillusioned ponies of this land realizing the two great alicorn sisters are all too mortal. Hordes of zealous followers of Zorypontha form mobs in the great cities of Fillydelphia and Manehatten, rushing in to smash and destroy the 'heathen idols' of Celestia and Luna. "Ponygans", they call the followers of the old faith, worshipers of false goddesses who they claim are only ponies like the rest of us. Their churches and cathedrals pack in new converts, while those of us Alicornists who remain watch as our temples and shrines see fewer and fewer visits. The Horsemaster followers tolerate us with a grudging contempt, even as our own numbers continue to diminish.
...the position of Stallions and colts continues to erode, as each new edict strips them of their rights to speak out against a mare, or to hold property. Alternate lifestyles and individual initiative are slowly being abolished, as the ponies who go against the herd are shunned and driven out. Even in our own Ponyville, I have seen a pair of outcast mares turn up drowned, after they had spoken out against the rising tide of strict morality the herd has embraced. And what does Princess Luna do to stop these travesties? Nothing, as she is still wrapped up in the grief of her sister's death. Our princess hides herself in her sorrow, as local noblemares seize power in each region. Loyalty to family and clan becomes more and more important, as friendship is spat upon and ridiculed as an outdated and illogical concept...
... I fear nothing can save our rotten society, even my own foals laugh at ideas the Harmony bearers once held dear. What can I say, when our school's teacher makes despairing remarks about an alicorn Princess who died as other ponies did? What can I do when my neighbors stand against anypony, who dares to speak out against the decay all around us? Our world is changing forever, and I fear it may not be for the better..." Twilight Glitter, This Wicked Generation of Equines
The Dreaded: Gypsy, the mysterious Romani unicorn, is feared by the local Dream Valley ponies. Justified for her really being spooky to ward off trespassers, especially since it's a dangerous world after Equestria's fall.
Dream Walker: Using the power of the Shining Star Lanterns, Twilight Shine's job is to enter the dreams of Ponyland's inhabitants and removes nightmares, just like what Luna did before she died.
Drowning My Sorrows: The first chapter of Tried and Trixie had Trixie and Booker in a tavern, drinking and depressed.
End of an Age: Seems like this is the Mother Trope of the mentioned fics due to the fall of Equestria and the death of Celestia and Luna marked the end of Equestria and the start of the Dark Times to the ponies.
Harmony Dies had started the end of all things that made Equestria, by the slaughtering of the Tree of Harmony.
Dawn of an Era: The Magnificent Six is basically this. With Cadence appointing new heroines for Ponyland, she ensured that the Dark Times in Ponyland will end.
Epic Fail: In chapter 43 of The Magnificent Six, we have the two witches Draggle and Reeka trying to stop the monster truck from reaching Misty Mountain by using their magic. They missed and hit each other with a boom.
Et Tu, Brute?: In the chapter Downfall part 2 in My Little Short Stories, this is what Spitfire and Soarin' felt like when Lightning Dust led her squad of Dream Valley's Lightning Bolts to sabotage the Wonderbolts as part of Dream Valley's plans to worsen international views towards Equestria. The Wonderbolts were never the same afterwards.
Faith Heel Turn: After the fall of Equestria, ponies view friendship and forgiveness as a sign of weakness.
Generation Xerox: In The Magnificent Six, we have six fillies who are direct descendants of the last bearers of the Elements of Harmony with similar, albeit slightly different, personalities and preferences.
Except Applejack is the same Applejack of FIM in all stories due to gaining immortality in Twilight Then, Twilight Now.
North Star is Daring Do's descendant. She is also an archaeologist.
Good Is Not Nice: Our Dream Valley heroes protect their herd and ponykind from evil, but the ponies after Equestria's fall have shunned actual friendship and forgiveness as something only the weak or sitting ducks use.
In The chronicles of the Horsemaster, Bz'ekre (the Horsemaster) placed the windigoes at the three pony tribes to wipe them out after becoming very angry at their fighting and lack of harmony.
"Enough! Ponykind has forgotten the messages of love and friendship I had created them with, and therefore must be cleansed from this world." The horsemaster decreed, regretting she had made this ungrateful, sinful ponies in the first place. "Therefore, I shall send a bitter cold to cleanse this world of their poison, and the other races I have mane may inherit the planet in their stead."
Götterdämmerung: The Fall of Equestria is essentially a long series of these, starting with the death of Celestia and continuing on to the erasing of everything Equestria had achieved.
Identical Granddaughters: Played with in The Magnificent Six. The main characters, Twilight Shine, Firefly, Posey, Surprise and Glory are Twilight Sparkle's, Rainbow Dash's, Fluttershy's, Pinkie Pie's and Rarity's descendants, respectively, and they look like their ancestors so much that Cadence usually expects them to be like their heroic ancestors. Applejack seems to be this as well, at the start, but is actually the exact same pony as we know in FIM. However, though they may look like their ancestors, they are very much different in terms of personality — Posey, for example, is terrified of animals and only wants to be involved with plants.
Kids Are Cruel: Some foals in Dream Valley seem to enjoy watching the adults (especially Sundance and Cheerilee) suffer.
Matriarchy: Zigzagged. Although not completely matriarchal, mares have considerably more power than stallions. Word of God says that this is mostly due to most stallions ended up turning very violent from the Grogar Wars onwards.
Although, he also said that when a war breaks out, the mares let the stallions take over leadership.
Moral Guardian: Moondancer. She was shocked on seeing Cheerilee (who is a time-lost Equestrian mare) 'naked' (only because she didn't wear a tail-bow). This trait is also the reason why most ponies in Dream Valley dislike Moondancer.
Oh My Gods!: Most ponies in this universe (who don't worship Alicorns) usually exclaim "Great Horsemaster!"
OOC Is Serious Business: One of the general themes of Moondancer's Misguided Mission, mostly due to Sun Shimmer's corrupting the residents of Dream Valley with false knowledge.
Precursors: The Penna are this to this world. They were very technologically and magically advanced for their time and could also magically create magical living beings. Their fall came when they created the draconequi and it backfired on themwith the draconequi turning against the Penna. The Penna-Draconequus war destroyed the Penna civilisation which left the ponies to rise in their place.
Redemption Rejection: After defeat, when Moondancer offered forgiveness and friendship to Sun Shimmer, Sun rejected it, furiously.
Southern Belle: Truly. She was from Mustangia (which is south of the Confederacy and Dream Valley) and she loves to dress up in style.
Take That: Moondancer's Misguided Mission is full of it: Molestia, Trollestia, Tyrant Celestia, Humans Are Bastards fics, Solar Empire vs. The New Lunar Republic, The Conversion Bureau, Doctor Whooves, Cupcakes, and Rainbow Factory.
The Fundamentalist: Let us just say that Tornado is a devout Zorypontist and looked at Alicornists with scorn.
The Power of Love: In chapter 54 of The Magnificent Six, Princess Cadence helped Twilight Shine and her friends by reminding them their loved ones to keep them from breaking the Rainbow of Friendship to defeat the witch Hydia.
Too Dumb to Live: The two witches Draggle and Reeka in The Magnificent Six are REALLY stupid! Their plans to sabotage Cadence's plans to create new bearers for the Elements of Harmony usually backfire on them.
Most fillies in Ponyville Generations: Spike's Story are this due to having generations in exposure with the enchantment put in all of Ponyville that makes visitors enter a dream-like fantasy, lowering the locals' intelligence and maturity. There are some exceptions though, such as Kimono and (G3) Cheerilee.
If you take the viewpoint that the New 6 are the heroes, it's still hard to deny that Applejack has a point that the present era is a Bad Future, what with the unequal gender rights, lack of tolerance, religious strife and other aspects that make it a full-on Crapsack World, compared to the mildly Crapsaccharine World that was the Golden Era.
On the other hand, even if you see Applejack as the hero — or at least a justified Well-Intentioned Extremist — it's hard to deny that the New 6 are really in the wrong when they point out that they have a right to exist too, even if they're not as perfect as their ancestors were.