This also includes spinoffs, such as Pokemon Mystery Dungeon, Pokemon Snap, Pokemon Rumble, etc, etc.
I have a few favorites:
Pokemon Ruby (It was the first video game I was ever allowed to play, but sadly it was only my brother's game)
Pokemon Mystery Dungeon: Explorers of Sky (I don't know why I loved this game so much... but I just really like it. I can't wait to get Gates to Infinity!)
Pokemon SoulSilver (It was the first Pokemon I ever beat, plus the first game I caught a shiny in.)