Mission 17: Journey Home. It begins with Edge commanding and leading you on a fly by where the Vice President addresses the nation. Then the Yukes attack, you're trying to cover the evacuation against at this point the toughest enemies in the game, then Chopper gets hit and holds out as long as he can until everyone escapes, but the ejector is stuck.
That's not the best part though. His death clearly leaves Wardog shattered, and they fight back, the enemy believes demons had literally taken them over and That One Level suddenly becomes a Curb-Stomp Battle.
Mission 27: Aces: the Tunnel Run, with the second most driving music in the game, surpassed only by the The Unsung War itself, flying at Mach 2 down the tunnel, and then Bartlet comes from the other direction.
Bartlett: I'm going to pass by you on the count of 3. One! Two! Three! (F-14A Tomcat screams by) YAHOOOOOOOOOOOOO!!!!
Nothing quite says "badass" or Game-Breaker quite like actually breaking the final mission. The first battle is supposed to last at least a minute. Using XLA As and a little skill this can be cut down to five seconds, with the game unable to keep up and the pre recorded dialogue running long after you've already won. On the plus side you get ample opportunity to hear all the second lot of dialogue uninterrupted.
The final mission. Especially the music accompanying the final part where you tear the SOLG apart piece by piece as it tries to crash land right in the middle of Osea. Nothing makes whatever you're doing more awesome than an entire Latin choir with orchestral accompaniment singing your praises as you do so.