The East Bay is a great option for startups on a budget. Cheap(er) rent, good food, lots to do, and many startup-minded folks. Emeryville is ~10-15 minutes away from downtown SF, so you won't be missing out on any major events in the city.
I second that. I grew up in the East Bay and thought it was a great places to live. Oakland gets a bad rap, but there are certainly some nicer areas where one could rent a house much more inexpensively than in the other areas mentioned. Also, there is lots of culture in the Berkeley/Oakland area, not to mention tons of great eateries.
Not just parking, apartments are a lot more expensive in SF too. Most events seem to be south bay but if you like driving then Berkeley/Oakland wouldn't be too bad I guess. I'd personally go for Palo Alto area but that's because university avenue is fun.
I would say that regardless of where you live, you should shed 2/3 of your cars. Cars are very expensive to own, and if you're a pre-money startup, you need to save money. Everything takes longer than you think.