Pretty much everypony has gotten at least ONE moment of glory, but Halo: Reach from the very first chapter stands out. DO NOT mess with Fluttershy!
Rarity also deserves credit. Her eye for detail lets her Curbstomp the invisible mooks that had been giving Applejack a world of trouble. Her showdown with the level's Boss was also pretty awesome.
Rarity's ability to quickly and efficiently manage details comes up again in both of the the Command and Conquer chapters, where she takes apartthe NOD forces and Rainbow Dash in Generals with surgical precision. Even her creating her base is noteworthy, described as 'watching her sew a dress made of ominous alien lightning'.
Pinkie nuking Twilight's base to the tune of "Ode To Joy", using the impact craters to make a smiley face.
Chapter five is made of awesome, as soon as the Rock Band game is turned on; from Rainbow Dash's passionate rocking to Fluttershy's sweet singing (That despite being amazing, was also So low that the microphone didn't register it, dragging her score down). But in the end, the cake has to go to Pinkie Pie, who not only scored a semi-perfect score on Dragonforce's Through the Fire and Flames, while at the same time playing as both lead guitar and lead singer, but also managed to do so - and save the rest of the band, who was missing almost every note - without breaking a sweat. Not counting the moments where she played with her elbows.
There's also Applejack (vocals), Rainbow Dash (lead guitarist), Pinkie Pie (drums), and Fluttershy (bass) playing "Colts N' Roses" together and managing to all get above a 90% their first time playing the game (Pinkie gets a 100%). Rainbow even gets a moment in the sun by going into Overdrive mode and hitting 96% of the notes.
Rainbow Dash managing to get around an 80% on Hard mode while being the vocalist and lead guitarist at the same time on her second time playing the game. While that's admirable, just the simple passion and excitement she has for it and the fact she just enjoys herself deserves mention.
Fluttershy, of all ponies, goes on a rampage after Rarity destroys her teleporters and sentry: she switches to Sniper and proceeds to tear through everypony in her path to hunt Rarity down. Twilight and Celestia are gunned down almost instantly, and she manages to kill every Red player at least once, along with Dominating Spike. It's only because she realizes that these are real people that she's curb-stomping, not AI, that she's finally stopped.