Alice Waters' fabled Chez Panisse restaurant. Opened in 1971, this place sparked a movement around fresh, locally grown food and is considered by many to be the birthplace of California cuisine. It's a tasty, expensive restaurant with a prix-fixe menu (downstairs, upstairs has a separate menu) that has spawned a lot of good things including the Chez Panisse Foundation and one of its pet projects, the Edible Schoolyard (a wonderful program at a public middle school a few blocks from my house - it really deserves its own post and photos.) The restaurant's cuisine and fame have also served as a launching pad for a host of amazing chefs and local businesses. It seems that if you work there (and don't totally screw up) you can pretty much write your own ticket. Some examples of successful local ticket-writers include Acme Bread, Metropolitan Bread Co., Pizzaiolo restaurant in Temescal, Greens Restaurant in San Fran (owned by Deborah Madison), Zuni Cafe in San Fran, César - a tapas bar which is right next-door to Chez (as those in the know call it), Eccolo restaurant in Berkeley, Bakesale Betty's shop in Temescal, Oliveto restaurant in Rockridge, and many more. If you want more info on this institution, check out Wikipedia's entry.
The Cheeseboard Collective. There are two halves to the Cheeseboard - the cheese part (they also sell delectable breads and baked goods, ice cream, and other fine fare) and the pizza part. Both are worker-owned and operated. The main down-side to the Cheeseboard is the extremely long lines. Also, I feel I have to note that the pizza, while delicious and fairly reasonably priced, never includes tomato sauce which is something I like to have on my pizza every once in a while.
They just renovated the pizza side of the operation and it's quite nice and a good deal larger (more room for tables and for the piano and the two- three jazz musicians who play there each night.) Pizza eaters still spill out onto the grassy median that divides Shattuck Avenue, despite the sign that warns "Keep off Median" which has been defaced to read, "Keep Off Media" (very Berkeley.)
The French Hotel. Although I have never been there, this place is always crowded, no matter what time of day. And sometimes there are even genuine Europeans sitting outside, nursing an espresso or latte. I can't vouch for the rooms but the sidewalk seating is top-notch (and tres Euro) and the coffee must be good.