Cerebus Rollercoaster: What originally started as a one-off comedic parody of a movie that might not have even existed has escalated into 30+ videos with several ongoing Storylines, Character Arcs, and an Interconnecting Continuity by multiple creators.
Clip Art Animation: The main six ponies (plus Trixie) are cutouts of leaked official concept art. Every other Ponyverse character is a fanmade vector.note (this includes Celestia and Luna, who appear in the actual movie, looking absolutely nothing like they do in these videos, though in those two's case it's because their concept art was never leaked) Everything else is random clip art and stock backgrounds.
Celestia and Luna's vectors were used long before we had any idea of what they looked like in the film. Hence the weirdness. -ZX
Credits Gag: Almost all the videos end with fake credits, usually containing names of celebrities or someone fired.
Jake Whyman (who started as a fan of ZXInsanity's videos before making his own) typically works the other two parodists - ZX and Blarghalt - into his credits, inevitably with absurd job titles. Those two in turn have responded in kind.
Twilight was supposed to be a servant of The Reapers indefinitely, but I ran out of ideas/jokes for her and thought it better if she was just the average main character (Well, what passes for average in these things!). -ZX
Halfway Plot Switch: "Politics" starts out with Twilight finding out she's a princess, then joyfully rampaging through Equestria. Afterwards, the story turns its attention to an apple and an orange about to face off in a duel, but are interrupted by Elmo.
Huge Rider, Tiny Mount: Both "Spike's Chill Evening" and "Vengeance, Thy Name is Apples" have Spike serve as transportation for Twilight despite being less than half her size.
Insistent Terminology: Partly to lessen confusion with the actual movie, partly because why not, the supertitle of these videos ("EQUESTRIA GIRLS") is always capitalized.
The characters "talk" by bouncing up and down, as like a child playing with a toy; their expressions rarely if ever change (in Blarghalt & Jakewhyman's episodes; character expressions do change occasionally in ZX's)
The characters' expressions usually change when something dramatic or important is happening. These moments seem to have been happening more and more recently. No idea why. -ZX
Mind Screw: You'll seriously go "What just happened?" after watching these.
Throw It In: If one of the three creators does something the others like, chances are it'll be referenced in the others' videos. Best example is Brad being Nicolas Cage; Jake Whyman came up with the idea and ZXInsanity declared it canon. Or Applejack only saying "Apples".
Unexplained Recovery: Spoofed in Vengeance, Thy Name is Apples; At the end of the episode, Jake Whyman and Blarghalt (or at least their avatars) confront ZX demanding to know why he killed off Applejack. He tells them not to worry as he's already found a satisfying and logical solution to bring her back. Cue Applejack miraculously poofing back to life with no explanation whatsoever to rapturous applause from the rest of the cast.
Wham Episode: "Vengeance, Thy Name is Apples". Applejack actually talks!