A few of my favorites:
Specialty's Cafe
101 New Montgomery St
San Francisco, CA 94105
Their food is only ok, but their cookies are excellent...they focus more on the traditional chunky, crispy on the outside, chewy on the inside cookies like chocolate chip, oatmeal raisin, peanut butter, etc.
Tartine Bakery
600 Guerrero Street @ 18th San Francisco, CA
I'm also a big fan of Tartine, where practically everything is excellent--the food/sandwiches, the cakes/pastries as well as the cookies. More of a French slant, and a broader range, such as Mexican tea cookies, macaroons, etc.
Miette Cakes
1 Ferry Bldg
San Francisco, CA 94104
This is a little French bakery out of the Ferry Building and their cookies are also excellent--very French...financiers, French macarons, etc.