When the entire Justice League show up during the final song! Also doubles as a Crowning Music of Awesome when they sing in harmony.
At the finale, Superman flies around the world to turn back time (both a Brick Joke and a shout-out to one of his movies), and then hurls Sweet Tooth's warheads into the sun, after Batman called him to apologise and ask for help.
Especially notable is that they take the most infamously Narmy line in Batman history and make it genuinely badass.
To Be a Man. Superman fighting Batman. In song. It's as glorious as it sounds.
Every time Sweet Tooth makes a candy pun, he actually pulls out the candy the pun is based on from somewhere on his person. As if stage acting wasn't hard enough, and yet Jeff Blim doesn't miss a beat.
Batman's speech to Superman about why superheros are awesome is enough to make any fan of classic comic books cry.