The fic has several running gags. Often they take the form of many short segments with different takes on the same scenario, separated by other segments.
- Twilight Waking up mid-step and promptly stumbling.
- Applejack trying various means of getting Trenderhoof to lose interest in her right off the bat. Some work better than others.
- Rarity and Twilight Waking up in rather bizarre variants, leading Rarity to ask "Twilight, why are we X?" It's gotten to the point where Rarity starts doing it for no reason in order to troll Twilight. And of course, Pinkie lampshades it:"Did somepony start a running gag without me? That's not nice."
- Luna coming up with bizarre ways to make her entrance in place of a Nightmare Moon attack.
- Celestia foisting off her royal duties onto someone else so she can go surfing, usually on the surface of the sun. This culminated in an incident where it took her less than 30 seconds to appoint the Elemental Harmony Gang as regents and flee out of sight... without checking to see if they were Awake first. (Most of them weren't.)
- Twilight asking what Ditzy's cutie mark is (and getting a different response every time)... which was then partially overtaken by scenes proceeding from the one in which she popped like a soap bubble.
- Twilight trying and failing to prevent Tirek (or for that matter, anyone and/or anything else) from destroying her library.
- Cadence being obsessed with matchmaking which it turns out she's been faking for a long time.
- Trixie and her... fondness for explosions.
- Trixie trying to tell a story about thermite, just to be interrupted by Gilda.
- Darth Vader cannot simply walk into Equestria. So every time he shows up in a Fused Loop, he makes sure to make a Big Entrance.
- Several Loops start with Nightmare Moon being defeated offscreen using bizarre Noodle Implements.
- Seaponies and Applejack's fear of Seaponies.
- Lyra's multiple personalities, and the bizarre situations that result from their interactions with each other and other characters.
- The Elements of Harmony being replaced by some other set of Elements (Elements of Capitalism, Elements of Style, Elements of Disco, etc.)
- A random pair of related ponies being the alicorn rulers of Equestria in place of Celestia and Luna (and one of the pair going Nightmare and being banished to some appropriate celestial body). Often paired with a non-standard set of Elements.
- "Princess Loops", where Twilight and some other pony defeat Discord and divide the governance of Equestria among themselves in some thematic fashion. Almost always, the other pony will eventually go insane in some fashion, and Twilight will have to banish them to the Moon for a thousand years.
