Alternate Universe: Golden Harvest explains the existence of these, mentioning how some alternate timelines and universes are different from others: some are offshoots of an existing timeline, while others are wholly separate. For example, the canon universe is a separate one (Golden Harvest is convinced that the events of "Keep Calm and Flutter On" could never have worked out in their universe) while the timeline where Fluttershy goes mad in her imagination and kills everyone is an offshoot.
An Aesop: Referenced when Pinkie Pie tells the story of the Batterqueen: among the many things Granny Pie taught her was that when telling a child a story, you always include a moral. In this case, she tells her audience that "Confidence and pride are the same thing."
When Fluttershy enters her imagination and becomes Fluttersleuth.
When the Crusaders ask Pinkie about things at the Sugarcube Corner, the page turns into a crayon-illustrated "Ask A Pony" tumblr layout.
Attention Deficit... Ooh, Shiny!: When trying to call Rainbow Dash and forewarn her, Twilight gets temporarily sidelined by the glee of discovering that the Sbale console actually knows how to spell every word she's using.
Being Watched: Twilight comments on this, unaware that Rarity is spying on her, while Celestia spies on Rarity, and Derpy Hooves apparently watches Celestia over her computer.
Pinkie Pie is convinced that Bon-Bon is actually evil, and that certain ponies are out to get her now that she's been named heiress of Sugarcube Corner.
Lyra also has theories she wishes to share with the readers, but the narrative seems to be deliberately trying to ignore her.
Cloning Blues: Pinkie's dream self has a mind of its own, which it thinks will disappear when she wakes up. She claims this doesn't bother her, but she's lying.
Cover Innocent Eyes And Ears: After a shouted line about baby-making from Rainbow Dash, Sparkler covers Apple Bloom and Sweetie Belle's... eyes.
Culture Clash: According to Golden Rule, while both she and Applejack are fiercely dedicated traditionalists, the farm pony's simply not cut out for being a princess of Prospit. In her opinion, she belongs on Derse instead; thus, she's extremely dismissive of her potential.
Golden Rule: I have nothing to live for but finding my people the best princesses to represent them, even with the apparently necessary inclusion of the Heir.
Death by Childbirth: Apple Bloom reveals this to be her mother's fate. However, she isn't actually sure of what that means.
Deliberately Monochrome: The Flashback to Applejack's barn at the start is orange-tinted, which Applejack finds very odd. Odd to the point that she's relieved to see it's normally colored when she checks on it immediately afterward.
Of course, this is Rarity we're talking about here.
Downer Ending: When Twilight interrupts her tale about the Batterqueen, Pinkie Pie idly thinks that it's just as well, as she cut her off at a good part, while it's implied that the full story doesn't end quite so happily.
Easter Egg: The fifth character selection option on this page. It's clearly visible on an older browser though.
Foregone Conclusion: It looks like the ponies will be successful in SBALE, and they may even save Equestria from being destroyed. Rarity may also go God Tier in a possible future.
Funny Background Event: During Pinkie Pie's retelling of the meeting between Love Lock and the Batterqueen, one member of the queen's retinue wanders off and becomes a crazy bee lady, in response to a suggestion from the forum. Complete with honey stall and derpy eyes.
RD: Look, Twah, I know you love your magic and all, but there must be a better place to practice your long distance tellykismesis. RD: Gesundheit.
Gilligan Cut: As Twilight Sparkle talks about how Rarity wouldn't risk Equestria being destroyed for an adventure we cut to Rarity watching Twilight with her own SBALE console. Which then cuts to Celestia watching Rarity. Which then cuts to Derpy watching Celestia.
Golden Rule is a 'compromise' based off of this: a 'wicked good queen'. As a result, she has anger issues, and difficulty restraining herself when she knows that snapping really isn't a good idea. Apparently Skaia isn't familiar with the concept of The High Queen.
Good News, Bad News: The 'both news are the same' variant to dream!Pinkie and sleuth!Fluttershy.
Pinkie Pie:"Now the good news is, I think I found the fifth member of the Midnight Crew!"
Pinkie Pie:"The bad news is, I think I found the fifth member of the Midnight Crew..."
Happily Adopted: It looks like the Mane Six all came from meteors. It's less than clear if other ponies also were made in the SBALE session.
The various player planets have personifications too, and attend Medium High where they vie for Skaia-sempai's attention in a multi-genre anime pastiche. (Golden Harvest has declared that reality "EXTREMELY hypoparenthetical".)
Hold Your Hippogriffs: Pinkie Pie is confused over whether or not she should say everypony when talking to the reader.
Hi everypony! Or wait a second, not everypony! Everyhuman? No, that sounds dumb. You guess you could say everyman, but why would you greet anypony with an old morality play? That's like the opposite of a party.
Hope Spot: Pinkie uses her Pinkie Sense and a bit of logical extrapolation to prove that, no matter how bad the Reckoning gets, nopony is going to die. Three pages later, Candy Mane is killed by a meteor.
Twilight realizes they could save most of Ponyville's population by evacuating them in their houses before entering the Medium. They have only a few minutes left before the meteors, no time to organise an evacuation.
I Call Her "Vera": Applejack has names for all her trees, and she's none too pleased when something happens to Martin. Or RD cracking up at learning his name, for that matter.
Imagine Spot: Twilight has access to a transcribed copy of Rose's FAQ. Like Kanaya in Homestuck canon, Twilight Sparkle imagines the Homestuck Kids as her own species.
Innocent Inaccurate: None of the Cutie Mark Crusaders know where babies come from. Apple Bloom guesses that you need some essence of life, and surmises it involves "vomiting into a bucket or something", much to the others' disgust.
"vomiting into a bucket or something" is the Homestuck fandom's general consensus on what troll reproduction might possibly be like.
Innocent Innuendo: While in Voice Mode and unable to see what's going on, Twilight hears AJ joke about playing a prank on Rainbow Dash. As the only skills she attributes to AJ off the top of her head are bucking and lassoing, trying to equate those to prank-pulling results in some interesting mental images.
Insane Troll Logic: According to Pinkie, Bon-Bon's reasons for wanting her dead includes "Bon-Bon doesn't know who Rarity is" and "Twilight snubbed Lyra back in Canterlot".
Les Yay: invokedTo the point that one command suggest that Sparkler is Ponyville's sole adult heterosexual mare (although there are a few more). The UST is clearly present between Rainbow Dash and Applejack, Twilight admits having a tentative relationship with Colgate, and Fluttershy is analysing her growing attraction to Rarity after befriending her, although she may just be confused since Rarity is her first real friend. (Rarity is confirmed as heterosexual.)
While reading Rose's incomplete account of her adventures, Twilight draws a lot of parallels between them. This insight concerns her, as she's not reminded of her present self, but of the mare she was before arriving in Ponyville.
Love Lock and the Batterqueen are both incredibly prideful, though Love Lock firmly believes in what she can achieve with her friends' help while the Batterqueen is confident about what she can do alone.
Obfuscating Stupidity: Carrot Top (aka Golden Harvest) deliberately messed up the banner during "Swarm Of The Century" just to make Twilight think that she was just a simpleton. In actuality, she's extremely clever.
Orwellian Retcon: The author claims to have removed several of Lyra's appearances in the past in retaliation for appearing in another Homestuck crossover. Derpy's and Ponet's names were also retroactively changed to Bubblecup and Goldenlight, respectively.
Other edits were made for consistency and less confusion.
Pokémon Speak: Cloud Kicker only says her first name. Turns out she's actually speaking a different language — Cloud.
Politically Correct History: A statue of the Mane 6 in the future shows them without horns and wings (except for Rainbow Dash, who is an exception as she's depicted flying).
Power Gives You Wings: Possible Future Rarity seems to have wings; it's likely that this is the result of going God Tier.
Pride: Discussed when Pinkie Pie first talks about the Batterqueen. Apple Bloom comments on Love Lock's hubris on making such a risky bet and says she's acting just like the Batterqueen. Pinkie tells her that when you succeed in taking that sort of gamble, you're called 'confident', but if you fail, it's called pride, though it's all the same thing.
Psychic Dreams for Everyone: As in Homestuck canon, but the twist is that Rarity awakened on Prospit before SBALE starts — or even before the Mane Six first met each other.
Smite Me, O Mighty Smiter: As Golden Rule knows her death is already preordained, she figures it's fine to call out and insult her goddess-creator over not being able to decide if Dash or Twilight should be the third princess of Prospit.
Sole Survivor: The time-traveling Mare-Do-Well!Rainbow Dash makes comments implying she may be one from a Bad Future.
Stalker Without A Crush: Medley, in regards to Rainbow Dash. Complete with taped-together photos and elaborate plans for the future and how they'll be the best of friends.
Stating the Simple Solution: After Applejack enacts a plan to get a crate out of a tree, one of the suggestions reminds her that she could've just bucked it.
Stealth Pun: Pinkie's land, the Land of Frosting and Treasure. Generally, everything looks very delicious, but Pinkie doesn't need to worry about her weight, because it's LoFaT!
Rainbow Dash: ...not that you believe in sea ponies or anything. You're not a baby.
Applejack: Y'all can trust me, Rainbow — element o' honesty and all that! Definitely not hiding any secret thoughts about you or anything!
Take That: The CMC had at some point attempted to make toy ponies. Both Applejack and Rainbow Dash remark on how shoddy and inaccurate the results are.
Pinkie Pie also mentions that in a certain line of toys, they only used five molds for a really long time, with all the other ponies being recolors. More molds appeared around the time of Cadance's wedding, which she laughs at: "Celestia and Luna do raise the sun and moon. And yet they couldn't start making alicorns until some measly princess of the Crystal Empire got married? Pfffff!"
You're Not My Mother: Golden Rule lays it on a little too thick with Rarity, who becomes deeply uncomfortable with how she speaks of her subjects and her insistence on hearing the message her mother recorded. When Golden Rule pulls out the 'practically family' line, this is her response.