Twilight's Establishing Character Moment. She bursts into the wedding half drunk and proceeds to take out most of the guards and Shining Armor and give a cheap shot to Celestia. But the awesome doesn't truly start until Twilight locks herself and Chrysalis inside a force field. The Changeling Queen takes the guise of Shining Armor (and later her friends) in an attempt to drain Twilight of her love... problem is Twilight only feels utter hate for her friends and family. What follows is 10 minutes of Twilight brutally owning the queen, with the readers only seeing the reaction of the wedding guests (they are so frightened they beg for Twilight to show Chrysalis mercy).
Twilight vs Rainbow Dash in the club. Rainbow spends the entire fight pretty much batting Twilight around like an unwanted toy. Only to realize Twilight was setting her up for a beat-down the entire time, and EVERYTHING that happened in that fight was part of Twilight's plan. Followed by Twilight giving Rainbow a rather impressive verbal beat-down that left the normally brash Pegasus quivering in defeat.
Doubt, the embodiment of the 6th Element of Harmony and the apparent puppet master of Twilight fall and transformation into a dark alicorn, verbally lays into Celestia and Luna in an epic "The Reason You Suck" Speech. What truly makes it amazing is how calm he is while doing it.
The death of Doubt and his rebirth as Faith.
In the sequel, Twilight's "The Reason You Suck" Speech to Rainbow Dash leads to the latter gaining the strength to wrestle control of her mind and body back from Loyalty's control.
Derpy performing an honest-to-goodness Sonic Rainboom while rescuing a plummeting Doctor Whooves and Dinky.
Let's not forget that unlike Rainbow Dash, Derpy didn't have gravity helping her; she was flying UP, fighting gravity, and STILL pulled off the Rainboom.
After Faith arrives on the Abundance, a massive airship he and Trixie stole, Loyalty begins to mock him, asking what long speech the silver alicorn is going to give this time. Faith cuts him off mid-rant by blasting him, summons a maelstrom, and tells his brother that because he tried to hurt Twilight and Trixie, Faith is done talking and he is going to kill him.
Spike pulls a Han Solo and bursts back into the final battle with Loyalty, helping to deliver the final blow.
When Twilight starts furiously stewing over petty details behind Faith's decision to blow up Cloudsdale to stop Loyalty from merging with itnote The city being an ancestral home for pegasi and a beacon of hope, Faith ignoring her objections, Trixie treating him like a king for it, etc., Shining Armor decides she's gotten away with enough wanton anger and shuts her up with a scathing yet well-deserved "The Reason You Suck" Speech, in the process comparing Faith's actions to her own when she attacked Queen Chrysalis.
Big Macintosh proving that he has balls of solid granite by calling out Queen!Applejack, knowing full well that she could easily brainwash or disintegrate him without a second thought, and terrifies her so badly she forgets she's an immortal demigod. The fact that this leads to Honesty's Heel-Face Turn makes this scene all the better.
The revelation that Pinkie was not swayed by Laughter's influence. Unlike the other Elements of Harmony, Pinkie saw through Laughter and realized that her games were pure madness. It goes to show that while Pinkie isn't exactly on the ball, she earnestly desires her friends' joy and was thus able to avoid being put under Laughter's thrall.
Trixie, for most of the story, has been next to Faith, acting as one of his potential love interests (the other being Twilight). Considering her rival for Faith's love is the Alicorn of the Stars, what can she do to compete? How about save Twilight from Doubt, who at this point has stolen Discord's powers and was in the process of disintergrating Twilight, and delivering an epic "The Reason You Suck" Speech. Trixie explains that while both of them are charlatans, Trixie at least knows she is a fake and uses her theatrics to get ponies to question the world. This causes Trixie to ascend and take Doubt's place as the new abstract of doubt.
Faith gets one in the third part of The Battle For Equestria. After Twilight and the princesses turn every member of the rebellion into an alicorn, the ponies give up their power and channel it into Faith, allowing him to gain back all the power he had before his death in Faith and Doubt. He proceeds to demand that if Doubt wants her revenge she come take it against him alone and rockets the two out of Manehattan.
Its a small moment, but when Faith grabs Celestia's throne with his magic and proceeds to beat Doubt with it is definitely an intense and cool moment.
The Abundance's finale. First, Generosity pulls a last minute Heel-Face Turn and sacrifices herself to save Equestria. Then, as the credits roll, Celestia and Luna arrive back at The Gate to discover their father, Lord Tydal, has returned from the dead. For fans that have been begging to see Tydal in a serious story, this was a dream come true.