Can you be more specific in area? There are some good shops in the East Bay like Vallejo (like Milt's Garage) which are too far for most people who live on the Peninsula or South Bay. Likewise there are a few good shops in Cupertino or Campbell that are too far for most people living in San Francisco. Bavarian Motorworks in Milpitas and TrackStar in Mountain View have good reputations, though I've never been to either. I had a PPI done at Dinan in Mountain View and thought they were good, though they are more expensive than most indies (but less expensive than the dealer). I also liked Schatz and Krum in Sacramento, but that only helps if you live out towards Sacramento/Davis.
Lowering my car's resale value one track day at a time...