I've lived in Hacker Fortress 2 months (los altos), visit frequently at Chez JJ for the last few weeks (mountain view) and have visited StartupHouse once to help someone move in(in SOMA).
Hacker Fortress and Chez JJ are both lovely. Chez JJ has been around a little longer, so they are more organized and hold great events; Hacker Fortress is a bit newer and more chaotic, but is more competitive on price. Both have great people.
Of the three, StartupHouse seems to be "trying" hardest in that the startup-ness is very in-your-face when you walk in. Key articles by Paul Graham and similar are hung up on clipboards, everybody is hacking away on keyboards, and the whole place has a sort of dark, moody, intense feel to it. I only visited once, so take my impressions with a grain of salt, but it didn't feel as friendly as HF and ChezJJ - most people didn't look up or seem to notice there were new people (maybe partly because there are so many people there), and the guy who showed us around was "on duty" and looked it. Whereas HF and ChezJJ felt like actual homes and not just places to hack.
In terms of physical building, HF literally feels like a fortress on a hill (huge mansion, isolated from surrounding houses, great view). ChezJJ is a cozy, comfy normal house on a street where the houses are close to each other, with fruit trees in the backyard (yum!). StartupHouse is a retrofitted warehouse and feels like it.
Whatever place you choose, I highly recommend staying in some kind of hacker house/hostel. The community you get from this living environment cannot be approximated elsewhere.