The original opening credits (up until episode 19) were visually inspired by Brooklyn Nine-Nine.
The Bird's odd speech patterns (talking too slowly, saying "Hello" too often) are modeled after early episodes of Home Movies.
Princess Celestia's voice is based on the Monarch.
Rarity is indirectly based on Korra's mom. Getschman originally wanted to make a The Legend of Korra abridged series, but that fell through. So he took the jokes he already had planned for Korra's mom (the voice and the obsession with spaghetti noodles) and applied them to Rarity.
Episode 3
Fluttershy appears to be singing (badly) the Doctor Who theme music.
In episode 9, Pinkie accidentally says a line from the My Little Pony fan animation Dusk's Dawn.
During a conversation about who the worst Abridged Series director is, Celestia, Luna and a royal guard mention Sherclop Pones, Greg Hoffman and Wacarb.
Episode 10
In episode 10, Fluttershy warns Twilight not to feed the bugs (parasprites) after midnight, a reference to Gremlins. (What makes it even funnier is that Fluttershy is giving the wrong piece of advice; the one thing parasprites and gremlins have in common is their capacity for self-replication, but Fluttershy only gives the instruction that prevents gremlins from becoming evil. The correct advice is "don't let them near water".)
Applejack refers to the parasprites as "darn tribblets!"—a portmanteau of Tribbles (from Star Trek: The Original Series) and AJ's trademark insult "niblet".
The palace guards' reactions are audio samples from "Wombo Combo", a particularly memetic Super Smash Bros. Melee video. (Jack Getschman also made several "Ponified Wombo Combo" videos prior to starting Scootertrix.)
Episode 11
The "Wombo Combo" audio samples from the last episode continue to haunt Twilight.
Episode 12
Apple Bloom quotes from Sun Tzu's The Art of War, which is apparently part of the curriculum at the military academy.
Apple Bloom's "Schlieffenpony Plan" for dealing with the Changeling and Crystal Empires is based on and named after Germany's Schlieffen Plan, their strategy for dealing with enemies on two sides in World War I. Both plans are unsuccessful, too.
Episode 13
There's one last "Wombo Combo" sample, when Rainbow Dash overtakes Applejack.
Episode 15
Pinkie quotes Yoda again, once more using the Force/Fourth analogy:
Pinkie Pie: Life breathes it. Makes it grow. Its energy surrounds us, and binds us.
Apple Bloom quips, "No battle plan ever survives contact with the enemy." This is one of many variations on Helmuth von Moltke's far-less-pithy original: "No plan of operations extends with any certainty beyond the first contact with the main hostile force."
Apple Bloom's raucous "get noscoped!" exclamation is a reference to thisCall of Duty internet meme.
The airship Black Häxan is named after the 1922 movie Häxan.
Episode 19
The Jessicas are all terrified of The Candymare, villain of the horror fanfic Something Sweet to Bite.
Episode 20
In episode 20, the changeling pony who mistakenly walks on two legs is Frostbright, the OC of animator Mr KupKake. (According to Getschman and Zimbauer, this wasn't an intentional shout out, but rather a convenient resource that they found online).
Episode 22
In episode 22, Celestia's line, "You've all done very well!" is a reference to Are You Being Served?.
Trixie's calling Twilight fat is almost certainly another reference to Ultra Fast Pony, which had whole seasons' worth of fat jokes at Twilight's expense.
When Discord mind-controls Pinkie into killing her friends, Pinkie starts reenacting Cupcakes (Sergeant Sprinkles). Then The Bird fails to follow the correct script, so the scene turns into a reenactment of Smile HD instead.
Royal Correspondence
The Scootertrix and Kanterlot universes are designated "Universe A" and "Universe 1", respectively—the same universe-naming convention used in the Futurama episode "The Farnsworth Parabox". note Apparently, this was an unintentional reference. EyesofEstranged, one of the members of TheKanterlot explained on Youtube: "Oh yeah! Forgot about that episode. We just gave ours '1' since our series came out first, and Scootertrix's 'A' since it's the better show."
Celestia's plan for trolling Lyra in episode 5 is a reference to the plot of the classic MLP fanfic Anthropology.
Spitfire's mention of "dancing on laughter-silvered wings" is a reference to the 1941 poem High Flight by aviator and poet John Gillespie Magee Jr.
Lord Tirek's "For I am Death, destroyer of worlds!" is a mangled reference to Robert Oppenheimer's reaction to the Trinity explosion:
I remembered the line from the Hindu scripture, the Bhagavad Gita: Vishnu is trying to persuade the Prince that he should do his duty and, to impress him, takes on his multi-armed form and says, "Now I am become Death, the destroyer of worlds."
While researching magical artifacts to fight Discord, Twilight mentioned the Amulet of Samarkand.
MAS Applejack retrieves the Spear of Nidhogg to use against Discord.
While panicking, Fluttershy uses a famous line from Aliens:
Fluttershy: Game over, man! Game over!
Fluttershy gets another one later, this time channelling Kevin McAllister from Home Alone:
Fluttershy: Hey! I'm not afraid any more! I'm not afraid any more!
Episode 26
Starlight Glimmer's test for the Mane Six is something of a Noodle Incident, but the few details the audience does hear sound remarkably like the cave of enchanted treasure from Aladdin.
Pinkie makes yet another Star Wars reference in ''Two Weeks Later". Just before encountering her arch nemesis, Pinkie says, "I sense something. A presence I've not felt since..."
Another Monty Python and the Holy Grail reference in "Twilight's Punishment". The bit where Twilight can't tell what word the owls find so offensive, parallels the scene where King Arthur can't figure out what word is causing The Knights Who Until Recently Said "Ni" to recoil in pain.
, a particularly memetic Super Smash Bros. Melee video. (Jack Getschman also made several "Ponified Wombo Combo" videos prior to starting Scootertrix.)