I also want to give a shout out to MacLeod's Books in Vancouver, though it has been several years since I visited while on other business. Not specifically specializing in horror, sci-fi or fantasy, but it was an amazing experience in the stacks-on-the-floor, who-knows-what-you'll-find sense. Many rare works. On that visit I found several out-of-print books of fairy tales, folklore and magick that I'd been seeking.
I'd previously heard about it from friends, but when I asked the staff at my hotel for direction, their answer was, "Sir, you don't want to go to that neighborhood." They were right about the neighborhood (major meth & heroin scene) but I was so happy when I walked in to see what it was:
Photos for MacLeods Books - Yelp
Photos for MacLeods Books - Yelp
Photos for MacLeods Books - Yelp