I was thinking Batman/Superman, but it always seems as though, to me at least, that its sort of a...I don't want to say one-sided friendship...shit, I don't know how to word what I'm thinking correctly to get the point across.
Superman always seems more appreciative of Batman than vice versa, but it seems as though Clark/Kal-El doesn't respect Bruce as much as the opposite.
Bruce always seems to have a relationship with everybody, so I guess I just took it as, Bruce makes everyone his best friend in their eyes, in different ways, but he respects Clark more than the rest, and that's why he constantly argues with him and fights (proves wrong, lol) with him.
Bruce has always been one that likes a challenge, and it seems as though he purposely does this with Superman because its the biggest challenge he could have, and in a way he's fulfilling a "keep your enemies closer" style of thinking, subconsciously...
There is a friendship no doubt, but I can't picture Bruce ever saying to Clark that he's his best friend. If anything I'd have to say Alfred is Bruce's best friend.
Spider-man and the Prowler
Black Canary and the Oracle
Venom and Morbius
Wolfsbane and Dani Moonstar
Ian Nottingham and Kenneth Irons
Blade and Whistler
Ironman and War Machine
Spider-woman and Nick Fury
Spawn and Cogliostro
Wolverine is close to Colossus, but I don't see them as best friends. Kurt is Wolverine's closest guy-friend, confidante and occasional spiritual advisor (as in Wolverine v.3 #7 or something.) Wolverine was once that way with Mac Hudson and Eugene Judd but they've grown apart over the years.
Kitty Pryde and Rachel Summers are best friends, I think. The concept of a "best" friend kind of faded from me after sixth grade, so I don't know if they see it that way, but yeah.