Bingo! We have a winner.

I live in South of Market and commute 37 miles south on Caltrain 4 days a week (work from home one day). It takes less than an hour door to door, and I sit on the train, relaxing or sleeping or reading the paper. On Friday afternoons, we have the "party car" where everyone brings food and beer. It's the best possible Friday afternoon commute in the bay area I can imagine. Even for those living in the burbs.

There is NOTHING like living in the City. Don't listen to all the suburb apologists trying to convince you that there is, indeed, some sort of nightlife in the South Bay, and that no, it's not really that bad living on the peninsula, even though you're paying SF prices. It's nothing compared to SF.

Yes, San Jose is the biggest city population-wise, when you count all the burbs. But as my grandfather (who lived there) used to say, San Jose will always be a one horse town. And yes, I have lived out there in the burbs, on the peninsula, and in the Sunset. It has nothing on downtown.

Go for SF. Avoid the Sunset and Richmond. South Beach, SOMA, Mission Bay, Potrero/Bernal Heights would be your best bet for accessibility to your work. You can work your way into Noe/Cole Valley/Tenderknob/the Marina depending on your tastes and commuting options. If you have a car make SURE that you also have a guaranteed indoor parking space.

Good luck on your move!