I'm not putting an order:
Intelligent Systems=Advance Wars, Fire Emblem, WarioWare, Paper Mario, Planet Puzzle League, Tetris Attack(Best development team Nintendo has pound for pound)
Treasure=Ikaruga, Bangai-O, Mischief Makers, Radiant Silvergun, Bleach DS, Gunstar Heroes, Alien Soldier, Rakugaki Showtime, Silpheed: The Lost Planet, Sin and Punishment, Astro Boy: Omega Factor, etc. etc.(By far one of the most underrated developers on Earth)
AKI=Every Nintendo 64 wrestling game released by THQ(Wrestlemania 2000, Revenge, Virtual Pro Wrestling, etc.), Def Jam fighting series, UPCOMING! Ready 2 Rumble Boxing Round 3! Oh Yeah!
Capcom=I shouldn't have to explain why they're on here or what they've done, unfortunately Capcom doesn't often have specific names for their development teams so it's hard to pinpoint which is best, Clover comes to mind, but they didn't make the fighting games, which is why I really enjoy them so much
Sega AM2=Virtua Fighter, Shenmue, Space Harrier, Daytona USA, Virtua Cop, After Burner, Rent-A-Hero
Criterion=Burnout, Black and the middleware engine RenderWare which powered GTA, Crackdown, Tony Hawk, and Mortal Kombat, among others
Visual Concepts=Sports games with 2K in the title, The Bigs
Nippon Ichi Software=Disgaea, GrimGrimoire, Soul Nomad & The World Eaters, Phantom Brave, La Pucelle Tactics(My favorite RPG developer)
Those would be the favorites.