When Garry and I moved to SF to start Posterous, we moved to SOMA since apartments are abundant and it's startup central. But I found little value in being near other companies. What I did find was a lack of food and culture.
Posterous first got offices in North Beach. I really LOVE North Beach. There's amazing food and it's a beautiful part of town. Plus Jam Legend is there.
+1 for the Mission. We love our new offices. Much cheaper than anywhere else in the city, most people can walk to bike to work, tons of great food, near Bart. We couldn't ask for much more.
However, one point of disagreement with Garry's map: you can't simply write off everything north of Market. Sometimes it seems like people south of market (SOMA and Mission) don't cross north as much as they should. There's a lot of city up there!
San Francisco is one of the greatest cities in the world. If you decide to base your company here, don't optimize to be close to Twitter. Optimize to be in a vibrant neighborhood with great food and great culture.
Believe me, even north of market, you will have no problem immersing yourself in startup culture and surrounding yourself with more tech entrepreneurs than you can handle.