The most organized store I've been to is easily Burbank Sportscards. You walk in there with a wantlist, and they'll be able to tell you what they have or don't have in minutes!
Now the most fun store I've been to is Bill's Sports Collectibles in Denver CO. Unfortunately, I haven't been there in around 15 years, but back in the mid-1990s, they had just a wide variety of cards and memorabilia.....Sports Illustrateds, Media Guides for all four pro sports, game programs, jerseys, autographed memorabilia, game used hockey sticks.....the list goes on and on! They of course, had cards from all eras. They were a bit cluttered, but it was just incredible to walk in there and see all the stuff they had!
Steve