I think my favorite sequence comes from Ace Combat 4: Shattered Skies. The story of the game is told as the recollections of a young boy "adopted" as the mascot of the main enemy ace. Over the course of the game, his recollections reveal that, as you play the game, the enemy pilots all begin to fear and dread flying against "the plane with the ribbon". (Your callsign is Mobius 1 and your plane is marked with a ribbon-like mobius strip.) For the final battle, you are put in the lead of "Mobius squadron" and sent to destroy the last enemy super-weapon. As you approach, you engage the last of the enemy ace squadron. As the two groups close, just before the fight begins, one of the enemy pilots says over the radio, in an absolutely terrified voice:
"Ribbons! They've all got ribbons!"
What's especially fun is, if you accelerate as soon as the mission starts, and time it right, you can lock on and destroy the lead plane just after after that sound clip plays. Puts a smile on my face every time....
A close second is Half life 2 : the siege of cellblock D-7. For the longest time, I'd backtrack to get more crates, tables, filing cabinets, oil drums, etc. to barricade myself in next to the machine gun ammo crate. It was fun, but it was also something of a chore. And then I saw a Let's Play where someone simply tuned the turrets around in their bays and then took cover in the empty one. It turned that whole section into such a elegant engine of destruction. One time, I left it going to make a sandwich. Literally, I made a sandwich. When I came back, Alyx was waiting to head on and I hadn't taken a single hit.