Figures all the games I really love would be placed against each other (boy, does that make me come off as a Nintendo fanboy). Anyway, not sure what I'm choosing so far, just going to try and figure this out as I post.
I'll immediately get rid of A Link To The Past and Super Mario 64. The former because I just don't really care for it (I don't dislike it, but it doesn't really do anything for me, the only Zelda games that have done something for me are Ocarina of Time, Majora's Mask, & Wind Waker [though I've never got much chance to play it (my brother owns the gamecube Zelda collection which comes with a demo of Wind Waker [a fifteen minute one I think] somewhere in the game and I've played the beginning at my cousin's once but that's it)]) and the latter because I preferred the DS release and besides my personal preference is side-scrolling platformers so while it's fun, it's not as fun as the other Mario games. I know when suggesting games I tended to go a little more "objective" but Mario games, most of them anyways, really only strive to be fun (and yes, games tend to want to be fun but they tend to have other objectives there whereas almost all Mario games don't want aim for other objectives, they are basically more refined versions of the essence of older games like Tetris & Pacman, where it served one purpose, fun, so yes, there is a distinction here).
This leaves me with Melee, DKC2, Majora's Mask, SMB3, & Super Mario World . . . games I really do love. Unfortunately, Majora's Mask & DKC2 are at a bit of a disadvantage here since they're the only games I haven't played in the past few years really but all made an indelible impact on me as a gamer so maybe that won't be a big deal but pointing it out now. I probably shouldn't remove Melee & DKC2 just because I prefer Brawl & DKC respectively, since this is only asking what's the best out of the list.
Okay, after typing out two long paragraphs and realizing that it took those two to cover three games, I've decided that it'll probably be my longest post on this site (which says a lot) if I continued with this method so I'll just stop and try and think this through internally then post my results. I've decided to remove Melee and DKC2 just because I prefer their sequel and prequel. I think I'll go with Super Mario Bros 3 after thinking hard about it. Mario Bros 3. has more variety (the different world gimmicks), funner boss levels, and is essentially perfect (in the All-Stars version at least [I also prefer the All-Stars version of Super Mario World, fuck palette swap Luigi]) and Mario 3 beat Majora's Mask because of personal preference. Both are essentially perfect games for their respective genres, but I prefer Mario Bros. 3 genre.