Well, I have to put it in, even if this fight created the whole "Batman can kick anybody's ass, no matter Who they are" fan base, but DARK KNIGHT RETURNS, Batman-Superman:

New Gods 11, Orion vs Kalibak final:

Sub-mariner, Triton, one of another forgotten greats:

Thor/ Grendell...THOR 377

Steve Rude's Superman vs Hulk:

And these were my favorite too

Vinny-

The Namor/Iron Man fight is from Tales of Suspense #81. It is reprinted in an old tpb, Marvel's Greatest Superhero Battles.

Here is another great battle:

Actually, it's from Tales to Astonish #82, and that is one of my favorite battles as well.

Some other favorites of the top of my head:

Spider-Man vs. Green Goblin in Spectacular Spider-Man (magazine) #2

Hulk vs. Wendigo vs. Wolverine in Hulk #181

Thing vs. Silver Surfer in FF #55

Dr. Strange vs. Dormmamu in Strange Tales #s 126 & 127

And +1 to Taavi for mentioning Negima, although I preferred the Kyoto battle to the one with Evangeline.

I also loved these:
Sorry about that

Most of the biggies have already been mentioned but here are some of my personal favorites. Forget the issues for all of these...

Namor vs the Dark Matter Hulk from one Peter David Hulk comic.

Also one Captain America comic that had two of the best fights in it was the one that featured the Red Skull v s the Kingpin and also Captain America (Fighting just after having his super serum removed from his blood) vs Crossbones.

Galactus vs Mephisto in Stan Lees and John Buscema's GN just to name a few.