I grew up going to Cody's, and I still hold it as the epitome of a great independent, community bookstore. It's clean, HUGE, well lit and organized. They host numerous author events, have a great magazine section, and the staff is always friendly, helpful and honestly enthusiastic.
But it's a little more than that too. You get the feeling that the store actually belongs to you and the community.. The website has photos of the renovations happening and their newest location, as well as work being done on a school they support. There's a great little corner (at least in the Telegraph location) of small and independent press publications, and I actually had a chapbook that I xeroxed myself on consignment there many years ago.
I especially like the shelf in the front with autographed copies of new books, it gives a great little kick if you're looking for a gift.