Let's not get it twisted guys. Even though this is a DC board, the fight between Spiderman and Doc Ock was the best comicbook fight ever.
I think this thread is about DC only, since the same thread creator opened the same thread in the Marvel forum.
Other than that, I agree with you.
Nothing from Nolan's Batfilms comes to mind sadly, so I'll go with the final fight from Kickass and...jeez, you'd think that superhero films would have more great fights really. I'll second Spidey vs Doc Ock and also Terry vs the Joker from Batman Beyond: ROTJ.
Also, not technically a superhero film, but I think Scott Pilgrim vs Todd the Psychic Vegan has enough superhero tropes to possibly qualify.
Spider-Man 2 has the best fight sequences in a Superhero Film, and it hasn't been topped yet.
He did not specify that in his OP. Let's let the OP make that call before we start drawing conclusions.