I was really impressed with Rome's public transportation system. Despite having the unique obstacle of having new Metro lines shut down because every time they dig they uncover something historic, Rome manages to move huge numbers of people around quickly and easily.
The Metro subway system is solid. It doesn't go everywhere, but the frequency of the trains is impressive. But the real strength of the system is having a central hub in the Termini station. You can get to Termini pretty easily from everywhere in the city, and once you're there, there's not a place in the city that's not reachable. It's also the home base for the nationwide train system.
San Francisco could learn a lot from Rome in terms of public transportation.