Plan on 90 minutes. I plan on 60 minutes door-to-door to make a 10am meeting. Add some time for the commute traffic.
My friend highly recommends the train. She lives in Palo Alto and gets on at the University station. Takes the express. She loves being able to do work, rest and read on her own while she commutes. She swears by it. Sounds like a great use of time to me.