For Indie comics and graphic novels, Comix Experience is legendary in San Francisco.
For years, I lived blocks away from the store and was able to stop in each week to pick up my books, and more importantly, get the newsletter.
The newsletter, actually a multi-page booklet, had reviews of upcoming comics and an order form which listed most of the popular comics on it. As a subscriber, I would fill out which comics I wanted, turn in the form and then the comics would be pulled every week.
However, when I moved back from Europe this time, I didn't end up in the Lower Haight, instead moving near the ballpark. This in itself made going all the way out to Divisadero a pain in the backside, but adding in a new job that requires a good amount of travel made it almost impossible to ensure I would even make it into the store more than once a month, making it difficult to ensure I would get the newsletter each month to fill out the form in time.
Because of this, I cancelled my account.
If your schedule allows weekly visits, or you just need a quick indie fix, you could do much worse than Comix Experience.