I heard Rogan mention on one of the recent PPV's that ATT was the top team (no pun intended) in MMA. I have compiled some of the top teams and their fighters. Feel free to add more or correct mistakes. For my money I like Xtreme Couture, but a few of them can have arguments made for them.
Black House is freaking awesome too, but I don't know if they will be around for much longers.

American Top Team-JZ Cavalcante, Thiago Alves, Wilson Gouviea, Denis Kang, Marcus Aurelio, Thiago Silva, Din Thomas, Yves Edwards, Jeff Monson, Gleison Tibau, Alessio Sakara

Xtreme Couture-Randy Couture, Forrest Griffin, Wanderlei Silva, Tyson Griffin, Martin Kampmann, Gray Maynard, Jay Hieron, Chris Horodecki, John Alessio, Mike Pyle, Frank Trigg, Mike Whitehead, Shawn Tompkins

Team Quest-Matt Lindland, Dan Henderson, Jason Miller, Sokoudjou, Ed Herman, Chris Wilson, Matt Horwich, Ryan Schultz

American Kickboxing Academy-Josh Koscheck, Mike Swick, Paul Buentello, Josh Thompson, Jon Fitch, Cung Le, Cain Velasquez, Christian Wellisch, Trevor Prangley

Jackson Submission Fighting-Georges St. Pierre, Rashad Evans, Keith Jardine, David Loiseau, Nate Marquardt, Karo Parisyan, Jason McDonald, Joey Villasenor, Leonard Garcia

Minnesota Martial Arts Academy-Sean Sherk, Brock Lesnar, Nick Thompson, Brock Larson

Black House-Anderson Silva, Nogueira Brothers, Paulo Filho, Lyoto Machida

Miletich Fighting Systems-Matt Hughes, Robbie Lawler, Jeremy Horn, Spencer Fisher, Tim Sylvia, Spencer Fisher, Drew McFedries

Team Punishment-Tito Ortiz, Rob McCullough, Matt Hamill, Kendall Grove, Melvin Guillard

Sityodtong-Kenny Florian, Jorge Rivera, Patrick Cote, Marcus Davis, Stephan Bonnar, Pete Spratt

Juanito Ibarra-Rampage, Cheick Kongo, Michael Bisping