I think you're going to need to make a choice between nightlife and not commuting. Palo Alto and Mountain View do have some decent restaurants, but they are still very suburban and don't have either the nightlife or quantity of great restaurants found in SF and parts of Oakland/Berkeley. I'm not thrilled with my daily commute to Palo Alto but I just know I'd be bored in PA/MV. Thus, SF is the place for me and I just accept the commute as a necessary evil.

If you do decide to live in SF it will be important to be close to a good freeway onramp or Caltrain. That means the Marina is out unless you want to add 15-30 minutes of SF city street traffic to the beginning and end of your commute everyday. Depending on the type of nightlife you like, I'd look in SOMA/Ballpark area, Potrero Hill, Mission, Noe Valley, Lower Haight and Hayes Valley. All of these places have great, albeit somewhat different dining and bar scenes.

Put another way, when you go out in NYC would you prefer the Meatpacking District or the East Villiage?