Housing on the peninsula is incredibly constrained so most people are priced out. Right now in the East Bay, San Leandro and Castro Valley are probably the best price points for square foot per $. Commutes suck from both places but they are equally positioned between valley and city giving you access to both.
If the bubble continues I would expect that both places will get priced out in the next 2-3 years. At that point you'll have to look at the Tri-Valley area (Dublin, Pleasanton, Livermore) for the affordable price points.
The Tri-Valley is actually quite a bit more expensive than the mid East Bay region (Hayward, Union City, San Leandro, Castro Valley). It's still cheaper than the Peninsula or South Bay, though.
If you're looking at the East Bay you're too late. Castro Valley and San Leandro were marginally affordable about 4 years ago. Now, you are probably going to need a salary of over $200K to support buying there. Dublin and Pleasanton have good schools so you'll need more $$$ out there. Livermore is probably still affordable to a mere mortal but I'd start looking further out towards Tracy or Stockton at this point.
If the bubble continues I would expect that both places will get priced out in the next 2-3 years. At that point you'll have to look at the Tri-Valley area (Dublin, Pleasanton, Livermore) for the affordable price points.