Naturally Murder by the Book's my favorite since I live in the Houston area and can get there fairly easily. I've been to many signings and events there over the years, and you're right. It's a great place.
In Los Angeles the place to shop for crime fiction is the Mystery Book Store, located in the Westwood area near the UCLA campus. That's where you'll find visiting authors, signed editions, collector's items, and the friendliest, most knowledgeable and helpful staff in Southern California. Any visit to L.A. should include a trip there.
Have to second The Mystery Bookstore. The owner, Bobby, is a great guy. Every year for the Festival of Books they and the So Cal MWA host a shindig in their store for authors and readers and handle signings throughout the weekend. Great store, great people.