Where are you going to be working? If you are working in or near san francisco, berkeley is fine. If you are working in the valley, the commute is going to suck.
I second Berkeley - Quick access to Bart from the Telegraph / Ashby areas - The neighborhoods can change rather quickly from block to block though - I recommend somewhere near the gourmet ghetto
I think I will have a home office for some time. I want to spend the most of my time for my startup and doing some remote job over the Internet.
I live in Cole Valley, which is quiet and quaint and right next to Golden Gate Park. I highly recommend it, but good luck finding an affordable 2 bedroom apartment.