Batman's final showdown with Owlman. Even though Owlman is Batman's equal in fighting skills, and is using Powered Armor, Batman manages to survive pull off a last minute win by sending Owlman and his bomb off the icy alternate earth.
It's also a Genius Bonus insult too: Throughout the movie, we've seen that Owlman is a classic nihilist, someone who clearly would be a fan of Nietzsche. Nietzsche is credited with the line "When you look into the abyss, the abyss looks back at you," so not only is Batman utterly defeating Owlman, he's mocking his philosophical standing at the same time.
And just for a hat trick—Batman didn't just pick the frozen world out of nowhere. Superwoman described it to him when she was taunting him during their fight, which is how he knew to look for it in the first place. Batman had to send the bomb somewhere, anywhere was better than Earth-Prime, but he still took the time to make sure he didn't sacrifice the few for the needs of the many, and he did it using a thread of information from a villainous monologue. Ladies and gentlemen, Batman at his best.
The fact that Batman fights his way through half the movie with a broken rib.
During the final fight, Flash throws Johnny Quick into a piece of equipment, shattering it. Johnny gathers up the shards of the device and throws them at super speed at the Flash who starts spinning around to deflect them. In a few seconds, Johnny runs out of pieces to throw and is forced to stop. At this point, Flash stops spinning to reveal that he has been catching each of the pieces that Johnny throws at him and has re-assembled the complete device which he hands back to Johnny.
Johnny Quick: Bugger.
When Aquaman takes on Captain Super;
Batman: Careful, Aquaman! They're stronger than you are.
Aquaman: That remains to be seen.
Even better, since it's soon shown that Aquaman is demonstrably stronger than Captain Super.
Batman takes on the Super Family in a power loader. Yeah, he ends up getting pounded, but it's still awesome.
When Good Lex reveals the blue Kryptonite (Ultraman's weakness, as opposed to green Kryptonite for Superman). Never before has the ever-predictable Kryptonite reveal from a Luthor ever seemed so awesome.
Ultraman: Blue... Kryptonite!
Lex: The only thing that can hurt you.
Ultraman: But... I...
Lex: Destroyed the last piece on Earth? True. But I've been visiting other Earths.
Jester's final line: "Okay, okay. I'm down to my last joke, anyway. But this one'll kill ya." KABOOM!
Black Canary using a point blank Canary Cry. "Wanna hear a secret?"
The League/Syndicate battle on the alternate Watchtower. Everyone vs their counterparts. They had been leading up to it all movie, and they didn't disappoint.
Owlman's final line as his universal bomb is about to detonate, with time for him to defuse it. It just sums up his entire character and motivation.
Owlman: (smirking) It doesn't matter.
Johnny Quick was by no means a good person, being a founding member of the "Crime Syndicate" and one of the most dangerous villains in his world, and yet when he's been told that Owlman is going to literally blow everything up, he doesn't hesitate to help Batman in his attempt to stop him Owlman, the attitude he gives off at the possibility of death really shows the type of person he really was.
Johnny Quick: He's talking about blowing up my world too and I'm not letting that happen!
Batman: It could be Dangerous?
Johnny Quick: The bloody universe is at stake, of course it's dangerous.
Even on the verge of death, he still asked if the world was saved and basically told Batman that he had no hard feelings towards him for practically sending him to his death if it meant that they saved the world. Johnny Quick was Villain, but died a Hero.
Johnny Quick: Did we save the world then?
Batman: We did.
Johnny Quick: And all that rubbish about me being faster, you knew this was gonna happen? (Batman remains silent)