Like many others on here, I would have to say Pokémon Snap and Pokémon Stadium were the best spin offs. I put in hundreds of hours into these games growing up - I just couldn't get enough of seeing my favorite Pokémon in 3D (lol).

Though I can't really compare them to other spin off titles like Mystery Dungeon or Conquest as I haven't played them. These two in particular look great and definitely worth looking into.

I loved PMD EoT, dat Temporal Tower music so good!

Pokemon Stadium 1 and 2

Pokemon Stadium 1. Seeing Pokemon rendered in 3d for the first time blew my mind as a child.

As a game, Snap.

Colosseum's soundtrack is the best though.

Also Hey You Pikachu is cool when you're 8.

Without question Colosseum and XD: Gale of Darkness.

Mystery Dungeon, it's a deeper series than what most other people think. They are better than the main games.
Explorers Sky is one of the most packed Pokémon games I've played and there are so many different ways to play it to challenge yourself as well.

Snap is overrated - Pokemon Mystery Dungeon is the best spin off series

The only Pokemon game I've ever played was Pokemon Puzzle League (which just happened to be a re-skin of Tetris Attack, the best puzzle game, EVER.). I guess I'll go with that.