Which side of the bay?
California Strength (Glenn Pendlay and team)
Ice Chamber is legit
Crossfit Oakland has some good people
Crossfit OneWorld I've heard good things about
Crossfit SF has KStarr (though he seems to be travelling 'round the world filming himself these days)
Jim Schmitz trains folks in South SF
Catalyst Athletics, of course.
Also, Dan John does workouts at Coyote Pt.