This is the high tourist season, not the cheapest time to stay in the Bay Area. But the best deal is Green Tortoise hostel. A little funky, but safe. Includes dinner every other night, breakfast every morning (make PB&J sammiches for lunch later!). They have laundry and full kitchen. Free internet.
http://www.greentortoise.com/san-francisco-hostel/index.php
The other hostels are good, just not as fun. Avoid staying in cheap motels in SOMA & Tenderloin districts.
There is an excellent hackerspace, noisebridge:
https://noisebridge.net/wiki/Noisebridge
2 blocks South of 16th & Mission BART
UC Berkeley and Stanford are up by San Francisco. Melno Park was where a lot of magic happened back in the day. I would try to find housing in the East Bay (NE Oakland, Emeryville, Rockridge, or San Leandro) and commute to work near a BART station. There is light rail between San Jose and San Francisco I think.
