1. Team Galactic. These guys are a huge part of why I love the fourth generation so much. I love that the group has this twisted Messiah complex of remaking the world in their own image in order to save it; they're well-intentioned extremists, which isn't something that can be said of any of the other teams. It's not about ruling the world, it's about saving it by transforming it into an ideal and, whilst the ideal might not be shared and the methods used may be questionable, isn't that exactly what the protagonist of any RPG does? Cyrus is a fascinating character, and they're a pretty solid presence throughout. The naming scheme is pretty cool, and the Legendary Pokemon they go after are easily the best ones in my opinion. Team Galactic think big. Rule the world? Screw that; rule the Universe. Trascend Space and Time. Great stuff.
2. Team Rocket. This is mostly nostalgia talking, but I love Team Rocket. They're the traditional "bad guys" of Pokemon, and I think of all the teams they're the most well-integrated into the region. The boss is a freakin' Gym Leader, for crying out loud. They practically own the Game Corner, and they indulge in everything from grand larceny to petty theft across the game. They're BAD. A tad underwhelming in the second generation, but it goes to show organizations don't just immediately disband when their leader vanishes; things carry on. It was nice to see them around again.
3. Team Magma/Aqua. They come as a set to me. I'm not entirely sure why Team Aqua would want to drown the world (last I checked, people can't breathe underwater and NOTHING good comes from living in underwater cities, on pirate ships, or small islands) but they serve as a logical counterpoint to Team Magma, who would be dreadfully boring and generic without them in opposition. One of the main reasons I'm quite keen on Emerald, despite disliking the third generation games in general, is because it involved both teams equally. Ruby and Sapphire (and their remakes by extension) felt lacking to me because of that exclusion of one of the teams to focus on the other.
4. Team Plasma. I found Plasma to be quite underwhelming; it would have been fantastic if all the talk of saving Pokemon wasn't an empty platitude, but in the end they turned out to be run-of-the-mill bad guys because, of course, you can't have serious morality clashes in a children's game. Plasma's general lack of presence in Black and White until the very end of the game was off-putting as well, and that lack of presence carried over into B2W2 as well. Although Ghetsis' battle theme was fantastically awful.
5. Team Flare. These guys are such a colossal waste of space. Their goal involves capturing Pokemon that have themes of Life and Death, and they make barely a ripple on the game, or on me as a player. I have very little to say about Team Flare, because I don't think there is really anything worth saying.