San Francisco is a gorgeous place to run but beware of weekends, when the parks tend to be really crowded.
There's a wide footpath all along the Embarcadero (Embarcadero BART station) if you like to run in the city. Otherwise, Golden Gate Park is lovely and there's plenty to see. If you have a car and you'd like a challenge, there are trails along the Pleasanton Ridge that are steep (and it tends to be warmer over there in winter, too).
Hook up with the San Francisco Road Runners Club or FrontRunners. Look out for runner groups on MeetUp, too. about 5 years ago