High level advice: - If you want a place that's walking distance, stick to the lowered number streets in that area. The Mid-Market area (5th and Market to 9th and Market) is not so great at night. That's why SF has given tax breaks for companies to move there.

- SoMa is not too far a walk from there. It's all newer developments, so they tend to be more expensive, especially as you move closer to the Caltrain station. But they're nicer apartments with amenities like an in building gym and if you're near Caltrain you can get down to San Mateo or Palo Alto on a train. Palo Alto + Stanford may be a fun day trip.

- You're very close to bart and muni there, so really the entire city and east bay are only a 15 minute commute away. If you're in the city for a summer, the Mission and Dolores Park area are awesome if you can snag a place. Great character, cheap food, some higher end food, and a neighborhood feel to lots of it.

This is something I'm also looking into, but I visited San Francisco this past September for a few days so have a sense of transportation and the the overall area.

Planning on moving my start-up there early next year and would like to find a room mate or a Hacker House that I can crash at from time to time.

try this : http://www.housingmaps.com/

Or any of these sites:

http://www.padmapper.com/

http://www.walkscore.com/apartments/

http://hotpads.com/

http://mapitat.com/

At least some of them allow limiting your search to places that are reachable by mass transit within a certain amount of time.