Daedalus normally stocks remaindered books in all categories (as well as DVDs and music CDs) at huge discounts, but you can also find a few newer releases (although at lower discounts). Often you'll find the slightly obscure mixed right in with the mass-produced.
Speaking only of graphic novels and related books, the selection at Daedalus isn't huge, but it is improving. The last two times I've visited, I've seen several publications by Fantagraphics Books, which is cause for celebration. I picked up Amazing Mysteries: The Bill Everett Archives Vol. 1 for $9.99 (normally $40) a few weeks ago. They also had Fire and Water: Bill Everett, The Sub-Mariner, and the Birth of Marvel Comics, but I already owned a copy. (Both are still available on the Daedalus website. Just click on the links above.) Daedalus also stocked Strange and Stranger: The World of Steve Ditko for eight bucks. You can imagine how long those copies lasted....
I also found a couple of other Fantagraphics titles last week: Action! Mystery! Thrills! Comic Book Covers of the Golden Age 1933-1945 and Setting the Standard: Comics by Alex Toth 1952-1954. The problem with finding these or any other graphic novel/comic book-related volumes on the Daedalus website is that there's no Graphic Novel category. Most of the time, these books appear (if they appear at all) on the site under "Arts - Visual."
To make things even more frustrating, not everything in stock at Daedalus is on their website. I recently found a copy of the noir murder mystery graphic novel Britten and Brülightly by Hannah Berry on the shelves for $3.98. I'd never heard of it, but for four bucks, I'll take a chance. But this was not on their website.
Neither was X-9: Secret Agent Corrigan Volume One: 1967-1969 by Al Williamson & Archie Goodwin, probably because all of the dust jackets were torn or ripped. But asking $15 for a $50 book? I'm in.
I've also seen isolated volumes of titles like Dick Tracy, Prince Valiant and many others. You never know what you'll find. So, if you're in the Columbia, MD area, you should stop in. If not, check out the website from time to time. Just understand that you're only seeing a fraction of what's actually there.