I don't live in the Bay Area, so I certainly make no claims on expertise. That being said, Chain Reaction, in Redwood City and Los Altos, maintains an informative Web site with articles to help first-time riders buy bikes. Here's their test-ride FAQ page, with links to more detailed articles:
http://www.chainreactionbicycles.com...etestrides.htm
I've been to both stores and found the staff in each knowledgeable and friendly. And the "Mike" who authored most of the articles on the site can be found in the flesh at the Redwood City shop—super nice guy! They also have deeper stock of built-up bikes than most independent shops. Good luck!
Edit: I just reread your original post and realized that you probably aren't in the market for a road bike. The FAQ I cited is specifically about testing road bikes, so you might not find it totally useful, though I think excellent points are made about buying bikes in general. CR does carry hybrids as well.