Light rail: comfortable, fast, moderately good coverage of the city. Price is fixed ($2 / ride)
Bus: Uncomfortable, slow, but excellent coverage of the city. Price is fixed ($2 / ride)
As with other suburban sprawl, the valley doesn't have enough density to pull off good service. Buses are infrequent and you may have a long hike to and from the nearest stop. Caltrain is fast and very reliable (IMHO, even fewer delays than BART) if you happen to be travelling between a handful of city centers (some stations have housing nearby), though they haven't decided yet how much service to cut due to budget problems (the worst case was going to be 8–5 commuter-only).
For the meantime, they found the budget to not cut any of the CalTrain service. I don't live in the Bay Area, but come over to San Jose fairly regularly. The CT is brilliant in my opinion for transit from SFO to SJ and saves hiring a car - long live CT!
The BART system is pretty good, but doesn't really cover Silicon Valley or the South Bay. San Francisco itself seems to be "pretty good", and is also a reasonable place to get around on foot. I could also see Berkeley being good, as it's fairly dense, but perhaps a bit less chaotic than San Francisco.