The movie is called Superman/Batman, so there are many. Special mention must go to Superman's final words to Luthor.
Luthor: I am the President!
Superman: Consider yourself * PUNCH* impeached.
Superman and Batman's fight against an army of supervillains. The comic book version has loads more, including lesser-known and obscure villains.
Batman takes out Bane in two moves, a well placed batarang & a round house kick to the head. A far cry from Bane breaking the Bat's back.
This seems to have been an attempt to stuff as much awesome into an hour-long plot as is humanly possible, and it does this quite well. Any scene where Batman and Superman battle anyone counts, period.
There's the mere fact that they used the real Power Girl, not an Expy. Bonus points for having her around Toyman, a thirteen-year-old boy, and the inevitable Most Common Superpower jokes that come with it. It loses points, since she is a Faux Action Girl and The Chick instead of her usual aggressive Big Guy form, but it is still something.
At least she killed Major Force. You can't claim that wasn't awesome.
There's Batman's grand finale, where he flies a giant robot made up to look like Composite Superman to destroy a Kryptonite meteor.
We can't forget little Billy Batson, blasted out of the sky as Captain Marvel by a wrist-fired rocket from Batman. Batman tends to the injured kid and says, "Say something." Billy's response? "Shazam!"