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Seconded, especially because it makes perhaps the best image possible: DC's oldest and most iconic hero is leading the final charge, yes, but he needs the most recognizable objects in Marvel to do it. A good way of pleasing both fan-bases while being incredibly awesome.
Thor vs Superman, both rounds. The first round, Thor smacks down both J'onn and Superman. The second round, Superman has Thor's measure, but Thor doesn't have his, so after a grueling battle, Superman manages to smack Thor down. As Aquaman gloats afterwards, Thor says that the next round with 'the Kryptonian' would go differently, implying that they're equally matched. A neat way to get around the usual fanboy rants on the subject.
And Superman says that "He... May be the single toughest opponent I've ever..." The missing word is fought, since the Avengers dogpiled him following that and unleashed a No-Holds-Barred Beatdown. Considering who Superman has fought down the years (Doomsday, Darkseid, Zod, Imperiex etc.) that's quite the accolade.
Flash and Hawkeye, both noted as being the comedy relief of their respective teams, saving the day. Even more awesome comes after this. Because of his actions, Hawkeye has been inducted as a member of the Justice League. Yes, Hawkeye is the only Marvel character to be a member of DC's premier superhero team.
Hal Jordan returns as The Spectre once Krona is defeated, forcing the twin Earths apart with his bare hands. Even Captain America is... impressed.
Hal Jordan's speech at the end of #3. Out of everyone there, he has the furthest to fall. And out of everyone there, he argues the hardest to Save Both Worlds. Someone get that man a miniseries.
I think Green Lantern: Rebirth got you covered there.
The scene where the JLA tours Marvel-Earth, and Batman spends the entire scene telling everybody via J'onn's telepathy not to interfere, that they should just observe and move on — until Batman stumbles over the Punisher attempting to shoot some drug dealers. Batman's immediate response? Spend twenty minutes beating the stuffing out of the Punisher off-camera, and get chewed out by Plastic Man after-the-fact.◊ Also counts as a Crowning Moment of Funny.
Aquaman also manages to stun and incapacitate the attacking Atlanteans. He makes a hilarious statement that they have minds a bit more complex than the average halibut. Luckily, Namor is half-Atlantean, so he just has a headache (a splitting one, though). Marrina isn't so lucky, though.
The moment when Captain America and Batman stopped fighting and decide to team up to find out just what exactly is going on. Or in other words, the foremost Badass Normal tactical super-geniuses of the Marvel and DC Universesnote Or slightly-above-normal in Captain America's case... teaming up to fight the bad guys. Really, at that point, the bad guys had already lost; all that remained was how close a thing it would be.
Doubling as a Crowning Moment of Funny, Vision comments that Red Tornado is just an android, so he'll stop him at its source by reaching inside and disrupting his machinery. Red Tornado comments, "Oh, will you?"
Vision: Hm? Inside him... Machinery and ... something moooooooooooooorrrrrrrrrrrrre! (Vision gets flung away like a rag doll)
This makes Thor perk up and view Red Tornado as a Worthy Opponent. He never gets a chance to test Tornado's mettle, though, because Firestorm traps him while he snatches the MacGuffins of the round (the items of the Demons Three).
A villainous example. Krona almost beats Galactus to death in 3 hits.
Just about the entirety of book 4 is a CMOA really. The biggest clash of super villains and heroes in scope with a different treat at every panel. It was mind blowing.