San Diego has somewhat of a "mehh" transit system. I mean its dependable, but only really accessable if you live near it. The bus routes are complex, plus there being two main transit districts (MTS and NCTD) plus smaller ones in the south bay make things even more difficult. But some things do work. Like...
The Trolley (LRT) works best downtown and along the way to the border station (blue line). They just extended it to through mission valley (green line), and another last extention is being planned to go to UCSD and University City up north. Heres a basic map of what the system looks like and the trains as well.
Meanwhile for a more reginal mode of trastport, you have the heavy rail "Coaster". It goes north-south along the coast and has been in service for about 11 years with some modest success. And a heres a basic map of the system. You may notice that the entire Zone 3 has only one station. Thats because almost the whole ride is a complicated and twisting path passing through canyons, valleys and Marine Airstation Miramar.
Besides those two and the buses, their really isn't anything else to use. Under construction now though is the "Sprinter" which is a smaller, almost LRT-like off-shoot of the "Coaster". But instead of going along the coast it goes through to inland cities of North County. It should be done by summer '07.