1. Smash 64
2. Touhou (series)
3. Melee
4. Pokemon X and Y (series - I say X and Y because the latest Pokemon game kind of "contains" the previous games in terms of Pokemon/moves/items)
5. Heroes of Might and Magic III Complete
6. Everything else
Part of me is pained to put Heroes of Might and Magic III as low as 5th. I think it's the most beautiful game ever created, in terms of... expansiveness. Completeness. It's not the same as the others to me. This game is like... books, movies to me. Because each map is its own world, and the game itself goes so much further than 99% of casual fans know. I don't think anyone who has gone far enough to complete truly beautiful masterpieces of HOMMIII maps, such as "Metataxer's Revenge" (German) or "Xiedu" (Chinese), could disagree. Even on small puzzle maps, each battle can be made into a unique and challenging puzzle, with a good mapmaker. It's pretty amazing. But I put it at 5th because I have to admit to myself I've been a little tired of it and stopped playing it very much. We'll see what happens to it in the future.
I pretty much never play Melee too, but I feel that's because I have nobody to play it with. I think I would like it a lot if I played it competitively. We'll see, though.
Touhou as a series might be a little unfair, but I didn't wanna put like 9 Touhou games on the list lol.
Nothing besides these 5 really stand out to me. Even very revered games I've played such as Ocarina of Time. Might seem strange to other people, but it's true. Maybe it's more accurate to say, these 5 trump everything else by far too large of a margin? I've played some other games, such as Sonic 3 & Knuckles and Super Monkey Ball 2, quite a bit, so those are potential candidates for 6th if I was nicer, I guess, lol. And there's some games I think could probably make it to 6th if I just played them more. Dark Souls, I can only play at a friend's dorm, so I haven't played it too much, but it seems very interesting, and honestly puts any 3D Zelda to shame in my opinion. Maybe I'll buy Dark Souls 2 when it comes out. And since I find Touhou very fun, I would probably like other shmups such as Mushihimesama Futari, but I haven't bothered trying them yet.