It's around 38minutes if you catch the 'bullet' train. I think the regular train is a little over an hour, although this doesn't include the time to actually get to the train station.
Yeah - it always takes longer to get to and from the station too. Sometimes it's hard to justify whether it is worth it! Personally I use ZipCar when I need to head down there now (which to be honest is rarely).
Yeah, I'm in palo alto now - but kind of want to move to SF. The crazy rent/finding a place and commute issue serve as a pretty strong resisting force though.