craigslist is definitely the best (i found my apartments that way), as the others said. make sure to check out the neighborhoods well -- the downtown and surrounding areas often change block by block, with very different areas very close together, and without knowing you personally (your likes and dislikes, comfort zone) i would say just get to know the neighborhoods so you can figure out where you want to be. there are many options fairly bikeable to Caltrain: SOMA, anywhere along the water (embarcadero), financial district/union square, chinatown, inner mission, outer mission, potrero hill, upper market, lower haight, north beach, nob hill, and more. you can find a neighborhood map - like this one http://justinsomnia.org/images/san-francisco-neighborhood-map.jpg. and as above, go to lots of places and meet lots of people. it's a time commitment but it will pay off!
my advice for craigslist hunting: start with postings about a week old to present. contact any that interest you. then check craigslist OFTEN (like every few/several hours) and write/call back to postings immediately - because many places are given by the order they were contacted, at least partially. if you really keep up with it you can find a place in a week or so, especially since you're looking at this time of year. if you do it less frequently or don't reply immediately the process can drag out over weeks and get really frustrating.