I am rather fond of SF's Muni system. Obviously it could use a few tweaks and improvements, but it's a great combination of trains and buses that get you anywhere in the city, so if the trains go down, you simply take one of the many buses that go to the same or similar places. And if you want to leave the city, then you take BART.
And if the trains are overcrowded for worktime commute, you can take express buses that stop only intermittently across the city - all for $1.50 a ride or $45 a month. Tough to beat that.
And don't forget the cable cars!
Oh yeah - and we have
www.nextmuni.com to tell me when the next train or bus is coming to my station so I don't have to leave my desk or apt until I know it's coming. Very handy and time saving feature.