I dont have experience as such but Im in a similar situation. I live mid peninsula and will also be commuting up to GGU most likely by train for preference (as I dislike busses etc and driving/parking is likely to be cost prohibitive.)
According to http://transit.511.org/tripplanner/index.aspx
it will take me about an hour and a half to Caltrain/Muni to GGU from Palo Alto station. It seems that there is a pretty wide range of options re starting times etc as the earliest option to arrive at GGU is listed at 5:30 AM. I sincerely hope I dont have to be on that train all that often
. I suspect that your times will be fairly similar, though if you are in the extreme South Bay it might be a touch longer than that.
I look forward to seeing you around Campus.