@de_lovely: These are probably your best options
A.C.T. is a LORT A, regional theater that does mixed to good work depending on the season. They certainly have the biggest budget of theaters in the area. Next season is looking promising, though.
Aurora Theater is right next door to Berkeley Rep. The quality of the productions is mixed, but definitely worth keeping on eye on every once in a while.
Berkeley Rep is definitely one of the best in the area. I would definitely encourage you to subscribe.
CalShakes is an outdoor amphitheater in Orinda. It's easily accessible by BART, then by shuttle. The productions are always usually solid,
Magic Theatre does really good work. They are located at Fort Mason Center. Most of their plays are world premieres, west coast premieres, American Premieres -- new plays.
Marin Theatre Company is roughly 20-minutes north of San Francisco. They are a LORT D, regional theater that also does good work, too.
TheatreWorks is a LORT B, regional theater in Palo Alto/Mountain View. The also specialize is contemporary classics, new works, and musicals. The quality is inconsistent, but mostly good.
There's also Z Space which is in the mission district of San Francisco. They do not have regular season programming, but they definitely program interesting productions. San Francisco Playhouse is very inconsistent with quality. As of late, the productions have been on the weak end of the spectrum. Hope that helps!