My choice would be Mystery Dungeon for 2 good reasons:

1.Rumble and Ranch sucked

2.All the others suck except for Snap and Puzzle League(which I liked.) And don't forget about Pokemon Ranger(that game was fun)
Bonus Reason
3.Pokemon Snap ALMOST made it but, that was due to Nintendo and Game Freak not making a seqeul. I mean why not make Pokemon Snap 2 I would buy it.

In fact Ranch(and Rumble) is so bad I'm not gonna include it in this poll.

Pokemon Stadium, well, because I haven't played any of the others, . I do agree, there has yet to be a good pokemon spin-off for the Wii. Nintendo and Gamefreak have to do something big that will really get people pumped, not just make a pokemon storage system and basic melee game. I won't continue, due to flame wars and what-not. O_o

I don't have a favorite most of them are pretty bad.

You forgot about Pokemon pinball!

Oh whatever
I would choose Pokemon snap because it was pretty interesting to play as a little kid and finding out what to do to get to the next area was pretty challenging for a tiny mind

Puzzle League was my introduction to Tetris Attack, which in my opinion is even greater than Tetris. It was also unique in its drawn influence from the anime, and its very nostalgic soundtrack. One of my most-played titles from the N64.

I liked the 1st-gen Pokemon pinball a lot, but it's not up there. I also liked pokemon puzzle challenge for the gameboy, but instead puzzle league is up there. That's what I voted for, since it came the closest.

puzzle league ownes

I would definitely say Mystery Dungeon, as there is always quite the storyline. And the repetitive parts hardly seem repetitive.