CSBG has a new top 25 up here. This is my submission.
10) Everyone vs Everyone else, including Captain Marvel vs Superman (Kingdom Come)
This fight is on my list because of the scale. It was epic. Love Ross or hate him, Kingdom Come became a classic because of this last battle outside the Gulag, with everything on the line. The panel of Superman there alone amongst the bodies of the fallen is iconic.
9) Batman and Green Arrow vs. Superman (DKR)
It doesn't ever get better. Many times before, many times after, Batman and Superman have fought, but it never stacks up to this one here. Messy, dirty, and decisive.
8) the Justice League vs Doomsday (The Death of Superman)
It's sort of a joke nowadays, but I still quite like this arc. Doomsday wades through the JLA, one of the weakest JLA incarnations. Beetle, Booster and Ice get really hurt, and Guy Gardner, Bloodwynd and Fire don't do to well either. Superman steps up to save the day. Doomsday would never again look as imposing, and Supes would be alive again by the end of the year, but the fight was really cool.
7) The X-Men vs the Hellfire Club, round II (Around Uncanny 200-210) Claremont and JRJR.
Again, no way this makes the top 25, but this fight was superior to their first meeting in the Dark Phoenix Saga in many ways. New members are on the team, and the Hellfire Club is ready to deal with the X-Men. Storm is depowered, and then Colossus and is neutralized quickly. Rogue is manipulated into stealing his powers and has to let him go or risk tearing his arm off as Leland sinks him into the earth. Just as the fight gets really nasty, Nimrod shows up. So awesome.
6) The Ultimates vs. Hulk (The Ultimates vol1, #6)
A newer fight, comparatively, but I read this issue, and then I read it again. It's great action, well choreographed by Millar and Hitch, and again, there is a feeling of tension here, because I didn't know what was going to happen. The first six issues of this book, capped off with this fight, made me a fan of Captain America like I never was before. Plus, the line "Hilk Smash Freddie Prinze jr.!" is solid. Gold.
5) East Coast Avenger Vs West Coast Avengers (2 part series in the annuals)
Eackos vs Whackos starts off as a baseball game between the two (Thor uses his hammer in place of a bat, for serious), but when The Gamesmaster and the Collector become involved, it turns into a one on one elimination fight to the death. A great fight just to see Hawkeye vs. She-Hulk.
4) Cannonball vs Gladiator (X-Men, with Joe Maduiera on pencils)
Cannonball is my favorite character, and seeing him take on The biggest, toughest guy in the universe in Gladiator was just pure eye-candy. This has no hope of making the top 25, sure, but it's a sentimental pick for me, and I reread this issue often enough.
3) Thing vs. The Champion (Marvel 2-in-1 Annual)
Quite possibly the single greatest comic book ever written in the super-hero genre. The Champion comes to earth to fight our greatest heroes in a boxing match. After easily wading through (through skill, or because they were disqualified for being morons) Colossus, Namor, Doc Samson, Hulk, Sasquatch, Wonder Man, and Thor, the Champion is getting bored with human. Then Ben Grimm, the ever lovin' blue-eyed Thing steps up, and gives the Champ the fight of his life.
2) Dr. Strange, Wong, and the Night Stalkers vs Dracula (The Montesi Formula)
Dracula is powered up, and he's coming. Doc Strange needs his allies to buy him some time to get ready, and they set up a gauntlet for Dracula. Drake, Blade, Wong, and Hannibal King step up, and then easily get stepped on by Dracula, before Drac falls for Strange's trap and a fight on the Astral plain. I love this fight, and I dream of of seeing it live action one day.
1) The X-Men vs the Imperial Guard ( The Dark Phoenix Saga)
Quite possibly the greatest all time team battle to be depicted in comics. Tense drama without gore or ultra violence. A team of heroes really put in their place. When people like Storm and Wolverine are dropped easily, it set such a tone of hopelessness, that as a young reader, I really felt that their back was against the wall, that Cyke and Jean would be hard pressed to hit that two-on, two-out 9th inning home run. When they didn't I was shocked.