In San Diego, there's the trolley system (run by MTS). They serve the downtown area, as well as some points east (they just extended it out to SDSU). At this point in time, the trolleys are unlikely to be of much use to you, but they've announced that there will be a line going up to UCSD. Whether this will happen before you or I graduate, I do not know. In the meantime, they may be of some small use to you if you need to get around downtown or are playing tourist.
The Coaster (also part of MTS)runs from downtown San Diego north to Oceanside. Some people use it to commute from coastal North County and there's a Coaster shuttle that goes between Mandeville and the nearest station.
In addition, one can travel with Amtrak or the like. Getting to LA by train is supposedly quite doable, but in general the train system in California leaves much to be desired, forcing many to fly (see planes).