By the end of chapter 9, Twilight, Pinkie Pie, Applejack, Rarity, the ponies from Mirage squadron, the Wonderbolts and Cutie Mark Crusaders all sing "Gotta Stay Fly" from Ace Combat: Assault Horizon (with slightly changed lyrics) and the entire ballroom cheers on them and applauds their performance.
Rainbow Dash performs a Sonic Rainboom to break inside The Burning Talon in chapter 10.
Scootaloo and Sweetie Belle get one in chapter 11. They use a home-built catapult to help defend Ponyville from the griffin attack.
Medley's Foe-Tossing Charge in which she defeats two griffins that held Rainbow Dash captive.
The way Rainbow Dash rejoins her fellow fliers by the end of chapter 12.
Rainbow Dash: I’m sorry to keep you waiting, girls. Let’s get the show on the road!
Garuda team's Big Damn Heroes moment in chapter 13. Heralded by this quote:
Talisman: We bring the fires of liberation.
One of the griffins bombing Stalliongrad is disposed of rather nicely. As Derpy closes in, he drops his bomb and tries to bug out... only for Derpy to catch up with him and send him tumbling through the air, out of control. She then knocks him straight into the ground, and into the blast of his own bomb. Boom.
There's one subtle awesome moment for Derpy and Medley in chapter 14. Using a broken piece of turret, Medley throws it at a griffon as a distraction before Derpy dive-attacks him and pushes the enemy toward Medley for an uppercut to the beak.
As reported by Flare Star in chapter 15, Blueberry fought against four griffins all by herself and even managed to kill one before being cut down herself. Talk about a Dying Moment of Awesome.
The whole chapter 17 can be seen as this for the ponies. Not only Canterlot is liberated, the ponies in other cities decide to lead their own counter-strikes, driving the invaders away.
Fluttershy vs. Night Raven. What seemed like a cruel No-Holds-Barred Beatdown at first, with Fluttershy being the victim, she managed to turn the tables after Night Raven revealed to her how much of a Blood Knight he is. The fight then ends with Fluttershy beating the crap out of Night Raven, then killing him via Neck Snap.
Most of the stuff Firefly does in chapter 19.
Zeakros sentencing Red Cyclone to die inside the collapsing Fortress Intimidation after his crimes are revealed to the griffins.
The final battle between Rainbow Dash and Gilda in chapter 20. Especially how Rainbow Dash turns her foe's Break Them by Talking tactic right back on her.
Derpy uses a guided penetration bomb to blow up one of the Exile battleships. Her sight is no hindrance at all. Plus, she follows the bomb drop with a great Pre-Mortem One-Liner:
Derpy: Here's a special delivery!
Even better, the other ponies defending Fillydelphia follow Derpy's example and attack with their own bombs...and sink the entire Exile fleet! The only things left floating are the lifeboats from the wrecked enemy ships.
By the end of the chapter, the Exiles attempt to nuke Fillydelphia using a cruise missile fired from Scinfaxi. Everypony pretty much gives up hope, but not Rainbow Dash, oh no! She channels her inner Colonel Bishop by telling Tornado Swirl to give his mounted machine guns to her, straps them to her body, then goes after the missile and shoots it down seconds before impact.
No mention of Mirage's arrival to the battle? Especially Rainbow Dash's Dynamic Entry, weaponizing the Sonic Rainboom...but not as a ramming attack; nope! She uses the shockwave to knock down a whole flight of Exile fliers! Capped off with a casual line:
Rainbow Dash: Sorry for the hold-up.
Fluttershy has a Freak Out at seeing the destruction the Exiles are causing, drops her lingering reservations about fighting...and delivering a powerful punch to an exile Pegasus while screaming in rage. Firefly remarks on how she will avoid making her angry at all costs.
Chapter 4 has two awesome moments as well:
First, a heroic one: Sunburst and his Phoenix squadron appear in the nick of time to prevent a bombing run on Ponyville. Also, he manages to defeat the flight leader by knocking him down, making him release the grip on the bomb he was carrying. After saying another great Pre-Mortem One-Liner, Sunburst throws the bomb at the falling enemy pegasus and finishes him off. May not be too much, but considering this Big Damn Hero entry is made by a secondary character, that really says something.
Secondly, a villianous example; Gleipnir, a huge grey dragon, reveals himself before the Mirage squadron and knocks them all out of the sky using shockwaves produced from his wings. Then, he goes to attack the ponies defending Ponyville (including Applejack and Twilight Sparkle) and... well, let's just sayhe easily turned the tide of battle.
Chapter 6 offers a couple of awesome moments:
Princess Celestia and Princess Luna use their magic to protect the whole city from an artillery attack, which, in turn, provides a significant morale boost to EAF troops and causes chaos in the ranks of the Exiles.
Tornado Swirl and Flare Star later destroy said artillery by bombing them. Flare Star quips another great Pre-Mortem One-Liner while dropping her bomb, clearly showing off:
Flare Star: Here, catch!
It gets better: Flare Star was dive bombing the Exiles, going near-vertical and screaming at the top of her lungs even before the one-liner. She wasn't just showing off; she was making herself an obvious target on purpose, just to taunt the Exiles before they died! And when she flies back up to Tornado Swirl, she's grinning so widely her teeth are bared.
There's a subtle moment of awesome between Flitter and Cloudchaser early in the fight. They double-team an Exile pegasus and ram into him from both sides at once, making him instantly drop out of the sky. You can almost hear the poor bastard's rib-cage go crunch!
Lightning Bolt using her Shining Spark to deliver a severe blow to Shockwave, saving Cloud Kicker.
Which is followed/countered by Shockwave surviving the attack! He's injured and has to retreat, but Lightning Bolt had been—successfully—aiming right at Shockwave's spine with her attack. He's a bad guy, but managing to keep flying at all after an attack that should have severed his spinal cord is unquestionably awesome.
Fluttershy ramming into Trickster and helping Blackberry in a struggle against him. Goes to show she is no longer that much of a pacifist.
The Meson cannon managing to hit Gleipnir in the wing and prevent his attack on the ground forces. Just before that, Rainbow Dash delivers a painful Eye Scream to the dragon.
Finally, another villainous example: Aigaion bombards Canterlot with his Nimbus Impact and shatters the protective barrier, forcing the ponies from EAF to retreat to the Crystal Empire. Oh and he also kills Firebolt.
Chapter 8 shows us exactly why Princess Celestia and Princess Luna do not engage in the war directly, unless it becomes absolutely necessary. Their combinedattack all but exterminates the entire Exile group that had come dangerously close to discovering the location of the Crystal Empire.
By the very end of the chapter, the last four remaining Exile pegasi have their flanks casually handed to them by an unknown gray flier, who is most likely either Blaze or Cipher.
"Casually handing their flanks to them" is putting it mildly: the first three are disposed of with one attack each very quickly, and the last Exile is reduced to begging for his life, only for the unknown pegasus to ignore him and snap his neck.
Chapter 8 also has Derpy blind an Exile pegasus with a snowball, stopping his attack run and leaving him wide open for an AA gun to shoot him full of holes. It's a simple, subtle thing; but it still cool nonetheless.
YMMV, but this could also double as a Funny Moment. Seriously, set up to die with a snowball? You can almost hear Derpy giggling when she tosses it at him, and the poor sap's lucky he died. Else he'd have to live with the humiliation of getting hit with a snowball in the middle of a dogfight.
In Chapter 10a, Lightning Bolt once again performs her Shining Spark, this time to prevent Gleipnir from destroying Cloudsdale. Her attack is powerful enough to nearly destroy the gem that powers up the dragon's armor!
In addition, her discovery that thunderclouds can be used as effective ways to eliminate Exiles fliers equipped with machine guns.
Chapter 10a also had a villainous one, for the Exile pegasus Bolt Burst: he manages to battle Flare Star to a draw, attacking her just in time to stop her from killing one of his comrades (who also happens to be a mare he loved), and cover their retreat. And to make it even more impressive, Bolt Burst is a regular squadron leader, not an elite or special-operations flyer like the Reapers. Given how casually Mooks are usually disposed of in this series, this speaks volumes for the guy's skill.
In Chapter 10b, Firecracker Burst is caught by the Exiles while she tries to distract them from Scootaloo, Rumble and Dinky, as they plant C4 charges on some hostile tanks. Despite being almost completely drained of her magic power and injured, she manages to pull one last gambit after the EAF troops attack Clad Hoof's units. Firecracker uses the last remaining ounces of magic power to blast Clad Hoof in the face with a stream of fire.
Hey, don't discount the Cutie Mark Crusaders managing to blow up those tanks! If not for them, the EAF forces would have been steamrolled. Bonus points for Button Mash picking up on their weaknesses just from video games.
In Chapter 11a, despite her arrogant attitude, Lightning Dust saves Quox's life (albeit not very willingly) and also tries her best to save her wingmates from being killed off by Orgoi.
In Chapter 11b, Princess Celestia aids the 1st Fleet by destroying burst missiles fired from Scinfaxi and later, with a little help from Princess Luna, reveals the huge submarine, allowing the EAF pegasi to sink it.
“This is the White Bird… I will protect you from the missiles.”
Chapter 16 gives an unquestionably awesome moment for the Cutie Mark Crusaders once again. Not only do they stand up for Miss Cheerilee and prevent her from being killed by Clad Hoof, but they pretty much insult him in the face for the Exiles' tendencies to hurt weaker ponies because it makes them feel strong. Then they casually mention that they destroyed Clad Hoof's tanks in Stalliongrad and the enemy commander goes completely ballistic.
Special mention goes to Dinky, of all ponies. After seeing so much bad things involve before her and with the threat of her friends and Derpy being poisoned by Cynocrine, she's had enough. She charges into the deadly gas cloud, breaks the container with the neutralizing agent and in turn, saves the lives of everyone present (minus Clad Hoof).
Chapter 17: An Exile messenger named Purple Prose arrives in the Crystal Empire, bringing a claim of Rainbow Dash's death. When pressed for proof, he produces photos. Everypony is horrified and distraught...but Lightning Bolt is able to remain objective and point out the photos could be fakes. Prose tries to counter that with a recording of Rainbow begging for mercy as she's excecuted, but by then nopony's buying it; knowing she'd never beg before an enemy. Too stunned to object (or just too bad at lying), the once-smug Prose is left stuttering and sweating.
And to top it off, Spitifre knocks him out and he gets dragged off to a cell.
Purple Prose: “... You dare threaten me? Mind your tongue! I’m an emissary! I am protected by diplomatic immunity and I will not hear anymore of your—”
, "Take My Breath Away" and The Anthem of Harmony