A second to the suggestion of Stones on Alameda Island.
For Berkeley, in the vicinity of Jitensha, is the Missing Link Bike Co-op. Skip the "new" shop on the west side of Shattuck -- you want to stop in on the east side of the street where repairs are done. You'll know you're in the right place by the spectacular display of SunTour pieces in the window (not for sale, great for ogling). There's more in the window (racing Olmo, last I was around) and more inside (Hetchins hanging high up for example), and often a retro-grouch or for the schmooz. And you're not too far away from Jitensha -- so go look in Jitensha's window.
(Missing Link: 1988 Shattuck -- closest cross is University. It's a block east of the University of California)
For another experience entirely, I've gotta bite my lip and suggest you stop into Team Karim used bikes on Telegraph. It has an interesting reputation on the local Craigslist. Interesting. Reputation. Interesting. Get through the congealed mass of mountain bikes out front and inside the door and head to the back. You'll find a bunch of road frames that are crap, then some hanging on the walls and in the crowded racks that make you wince for the lost glory of them. All the good kit has been stripped off, probably sold. The stuff slapped on in its place -- all wrong. The prices are nutty for what you'd get if you were fool enough. You'll also get the hard sell -- "Tell me what you're looking for" -- 'cause browsing really isn't welcome, or you might find a bike you'll claim you already own or may in fact already own but haven't seen in a while. Or so our anonymous Craigslist friends would have you believe. Interesting. Reputation.
TeamKarim.com on the web. 2800 Telegraph, south of the UC campus by several blocks.
That's it for my East Bay knowledge. -- Dan Kehew, Davis CA USA