I haven't seen other groups than TR in the anime, and I really don't think they are any good there so I'll go with the game and manga perspective~
In the PokéSpe manga, all villain groups are pretty sinister and cool. All have their reasons for doing things. Giovanni wants to stop Mewtwo and find his son, Archie and Maxie want supreme power and change Hoenn (iirc) and later Archie wants a wish, Neo Rocket is manipulated by Pryce to find Celebi, Cyrus is evil for real and wants to recreate the universe...
Come to think of it, Team Galactic is the creepiest team. While Magma/Aqua can be reasoned with, and TR are petty thieves or at least criminals, TG has mindless followers and an ultimately sinister goal of destroying the region and enter another dimension. They are so creepy. Never played through a Sinnoh game fully, but in the manga they are downright evil, freezing people into another dimension and blowing up the lakes and stuff. I thought Archie was creepy, but this...
Then there is Team Plasma, which I think is the most interesting of the teams. It has a story and goal, moreso than the other ones. Bar Magma/Aqua perhaps. The whole thing with Ghetsis and N is smart and really, I should finish my White version already to see~
Team Flare, I don't have any clue about. They don't seem too good or cool really :p
Still, TR with Neo Rocket from the manga and later even in the FR/LG saga might be the best villain team still. Rocket and Plasma can get a shared first place from me.