I feel you. I'm a grad student at your rival school in the East Bay. Grad student pay sucks, huh?

Sorry, don't have system designed for your setup. But these are some things I've picked up on travel since I've been here. Hopefully some of this will help you some, but it might be redundant too, in which case I'm sorry.

Southwest is probably your best option and basically designed for our situation. Low fares booking in advance and easy to pick up rewards. For this area, if there's someway you can make it out to Oakland, it might give you a bit more flexibility, since I believe WN operates more flights out of OAK. If you can't get to a car and you don't really care too much about time, you could get there thru CalTrain/BART. It'll probably cost you an hour more than getting to SJC by CalTrain. Oh yeah, get Ding! if you haven't already.

For some last minute trips, United E-fares can be pretty good. Every Monday night at midnight (actually, sometimes later. search for united.bomb) they come out with E-fares that apply for that week and the following week. Trips have to be Sat departures and Monday or Tuesday returns. Fares are around or slightly higher than early booking, but if your past that 14 day window, its worth checking out. Destinations vary from week to week, so its a bit of a crap shoot. The plus side is that since SFO is a United hub, there's usually a fair selection.

Don't know much about American, other than they tend to have cheap flights out of SJC. Hopefully another board member can comment on that.

I mostly use WN and UA. I have the UA MP College Visa. No annual fee, 1 mi for every $2. Not too useful at racking up RDM. Kind of like that jewlers axe in Shawshank Redemption. Maybe do a search for the Citi PrimierePass or other cards on the board with travel rewards points. Although, I usually try to defer to cards that give me cash back (ie Amex BlueCash)

I do look through the posts for UA MP promotions, like the NetFlix one a while back, or the 125 mi from Safeway. As mentioned in an earlier post, if your within 12mo of graduation they'll give you 10k miles if you mail them your transcript. You get 3k miles if you sign up, and if you do it via referal from a current MP member, they get something like 1k miles too. Through odds and ends, I have earned one short hop from SFO to LA saver award for an family emergency. Later on, if you end up flying to conferences though and the univ. or research money pays for trips and they end up being fairly long, it might be worth it to book it through a legacy carrier and pick up miles vs. segments. I'm earning about 10K miles from two conference this winter plus the miles on my card plus EasyCheckin bonuses.

Otherwise, Kayak and Farecast are my price searching friends =)

For Tahoe, IMHO, it's probably best to just find a group of friends and drive. The airport is in Reno and you'd have to get out to the lake. Not a total pain, but it's more fun and cheaper to all go up, rent a cabin (I think you guys might have a student one you can rent as well?) and go about it that way. Tahoe can also easily be a day trip as well.

That's my $0.02. Hope it helps you some!