I did my masters at Berkeley, and have since moved to the peninsula for work.
It can be pretty hard to find a nice apartment in Berkeley, but there are usually tons of people looking for roommates. I showed up two weeks before classes without anywhere to live, but after an hour on craigslist and a few phone calls, I'd found a room on the south side and moved in that day.
On the subject of public transit, one perk at Cal is you can get a free AC Transit bus pass sticker for your student ID; it even works on the transbay buses. Some students never use it, some live by it. Also, nextbus.com has a live tracker that works on cell phones.
ursprache: If one of you is driving, parking is a bit easier at Stanford, for whatever that's worth. OTOH, the bridges can be traffic bottlenecks.