As a newsman at San Diego's #1 news station, I may be qualified to help.
I would recommend Mira Mesa. It is cheap and reasonably nice and about 30 minutes from UCSD by the 921 bus, or 15 by car. I would highly recommend softening your stance on roommates. With a roommate, you can get a decent two-bedroom in La Jolla for $700-900 depending on the quality.
I actually have a roommate (GF) so I'm paying half of the 1br. But thanks, keep the info coming, it'll be useful to loads of people since SD's main drawback is price.
EDIT: Checked out Mira Mesa. Definitely good advice. A bit far from the Whale's Vagina, but I'm not much of a pub-goer, and can probably swing grad student housing until my courses are done (after which the commute isn't much of a big deal).
For those who are looking at this thread later on, Mira Mesa to UCSD is 20 minutes by car (not 30 minutes), and an hour by bus. Costs in La Mesa run $900 for a 1-BR, 1200-1500 for a 2 BR, and around $2k/month for a mortgage (3 BR/2 Bath, with minimal work).