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My favorite is Explorers of Sky. Although Red and Blue Rescue Team were great, they didn't have as good as a story line as Sky did. Plus Sky had better Pokemon that you could be imo.
My favorite spin-off Pokemon games of all time is XD: Gale of Darkness and Colloseum.
My favorite hand-held Spin-off Pokemon game is Pokemon Red Rescue Team. It's the only one I've ever played. It was also addicting and fun to waste time with.
No one's mentioned the Pokemon Ranger games... or the Pokemon TCG games on the GBC... Those are my favorite spin-offs, as well as Pokemon Puzzle Challenge.
Though Pokemon Ranger is more of a love/hate - I like the graphics and the atmosphere of everything, but there are times when I'd like to throw the DS at the wall (Salamence, Charizard, etc.)