Ok, I'll try to answer. SFO is the closest, but usually costs more. Oakland is convenient. Not sure about San Jose - never gone out of there (but have gone from SFO and/or Oakland to LAX or Burbank). Both airports in SF area (SFO and OAK) are fine. If you fly to SFO, it may be more expensive in air fare, but the transportation can be cheaper (shorter distance). When you go to Oakland, the fare is cheaper, but the transportation (car, bus..) is more expensive (going a farther distance). Of course, you can take BART from Oakland (not from SFO), but it's a pain if you have lots of bags or heavy stuff. I think when I came to interview, I flew to SFO from LAX.
I personally would do the trip in 2 days because I am not a morning person and most activities start at 8AM and end between 3 and 5PM. You are really tired by the end of the day - and there's a good amount of "down time" when you're not doing much - interviewees usually hang out in the student lounge during those times. Granted, your time frame depends on your schedule and ability to take time off. You could always fly up the night before, stay over, interview and fly back the next day. That in effect would only take one day, but would make you more rested.
I think rest and relaxation are key before any interviews. So, the more time you can get to become acclimated, look around, relax, and rest, the better. Hope this helps. Feel free to email me with specific questions. Good luck!
-- Becky