My favorite thing about riding in the bay area was that you could do one way rides and take the BART back home. I did syline blvd in the East Bay alot. then cought the BART back to San Leandro. The Dumbarton Bridge was mentioned above, what is great down there is to ride out on the levees (sp??) that take you way out in the bay, on a warm, calm Sunday morning nothing is more pleasant than that. If you want to climb a hill, Mt. Diablo is a nice climb, it's an uphill slog for 10 miles or something, but at a doable grade, with the kicker at the very end, I'd ride there then BART back.
As for Dirt in the Region Parks you need a bell on your bike. I rode mostly in Chabot park with was a nice place.