Batman at a wharf trying to get rid of the Cartoon Bomb, finding nowhere to dispose of it without running into things like a Salvation Army marching band, a woman pushing a baby carriage, nuns, and even a family of ducks. Batman in frustration:
"Some days you just can't get rid of a bomb!"
This recently became utterly hilarious in hindsight given that The Dark Knight Rises recycled this particular scene as its climax.
At the very end after the Security Council is re-hydrated. The way West delivers those lines are just plain HILARIOUS.
It gets better. Right before they leave, Robin and Batman glance back, watch the Security Counsel bicker in their new languages, and then turn away in a manner that suggests "Yes, we are definitely done with this. Let's leave, but inconspicuously." And then they leave. Out the window.
While fighting off the baddies out-of-costume, Bruce Wayne knocks one goon onto a spring-loaded catapult and sends him flying out the window (as a stiff dummy) and into the sea. The goon then explodes.
During the big fight on the submarine, Catwoman decides to throw her cat at Batman. Bats catches it and runs around with it, trying not to get hit, and finally tosses the kitty into a life raft and gets back to the brawl.
Batman: Bon voyage, pussy.
BAT.SHARK REPELLENT. Even better, the shark explodes immediately afterward (not that it makes any more sense, but the shark had a bomb in it).
Selected from an assortment of sea-life repellents, including Whale Repellent.
The Penguin trying to trick his way into the Batcave as Commodore Schmidlap. How well does his disguise work?