I've been stealth camping off-trail in the Bay Area for years and have never had problems with cops or rangers (not for that reason, anyway). If you're discrete and out of view of the trail, you'll be fine.
It's particularly easy in the state parks (Marin Headlands, Mount Tamalpais Watershed, Samuel Taylor State Park, etc.) because the budget cuts have all but eliminated ranger patrols. Beaches are great, too. I've camped dozens of times at Rodeo ("Cronkite") Beach and Tennessee Beach in the north and on Ocean Beach in the south. Free camping is easy in the Bay Area if you know where to go.
I've got some other tips on wilderness squatting the Bay Area on my blog hobocynic.blogspot.com.
Happy trails,
-Rasmus