My favorite shop to browse in is Cupertino Bike Shop. It is full of italian classics, and the owner has been collecting bike parts for a long time. Kinda neat history leccon if ya will. It is truely a clickish roadie shop and I rarely get by there but when I do I always enjoy the place.
For Mt Bikes its Trailhead Cyclery in San Jose, also the closest shop to my house. Purely a speciality shop, and one of the best parts stock in the area.