The scene when A.J. uses the Armadillo's mounted gun to blast through their Shuttle.
Dan Truman:(to General Kimsey) This is one order you shouldn't follow and you FUCKING know it!note (Some English edited-for-television versions of the film have him saying "Freakin'" instead but it still counts.)
Colonel Lev Andropov reminding us that Cloud Cuckoo Lander or not, he's still a veteran cosmonaut by repairing the second Armadillo—while it's flying over a gorge in Zero-G—so it can make the landing safely. And he's doing this while clinging to the outside. Bonus points for his Badass Boast prior to all this:
A.J.: What the hell are you doing?!
Lev: I am the only qualified astronaut here, and I am saving your American asses!"
"Houston. You're not going to believe this but the other Armadillo has arrived."
After the world realizes they're saved, there is a shot of a new generation of kids inspired by NASA, representing the future's likely renewed interest in space exploration, running past a mural of President Kennedy, who started the whole thing.
"We Win Gracie!!!!!" Cue the movie's money shot and Bay's signature, the asteroid going up in a hugeass explosion.