And since Silicon Valley is slowly moving up to San Francisco, it's worth noting that BART never runs enough trains to meet demand. It's pretty infuriating for those of us who live in Berkeley/Oakland.
This seems to be due to the sudden combination of 1. budget cuts and 2. a big tech boom. So there were suddenly significantly more riders just as service was taking a hit. Bad combo.
Last year I started commuting into SF again from the East Bay after a 4 year break and am still surprised at how full the trains are. As recently as 2007/early 2008 it was much easier for me to get a seat.
(This is partly down to the fact that BART is funded out of so many different pots of money, including federal, that it can't just expand and contract in perfect sync with the local economy.)
8-car (or even shorter, sometimes) trains at rush hour are also infuriating. But mainly what BART needs is better software so they can shorten the headway.