The marriage of a good book and a whimsical book designer is a beautiful thing. The five-legged Knopf dog on the spine of hardcover editions of Geek Love (a novel about circus freaks) is my favorite example (click to see it bigger):
There are a few Angela Carter paperbacks in which the Penguin logo plays with the design, like these (again, click to best see the Penguin's quirks):
The classic of the art may be I, Libertine. The book was initially conceived of purely as a hoax in the mid-1950s to protest then-current ways of creating bestseller lists. You have to read the story. Part of the story is all the in-jokes on the cover (designed by an artist who went on to help design Alfred E. Neuman).
There are some good non-cover book quirks, too. My favorite is from A Heartbreaking Work of Staggering Genius by Dave Eggers. Now some people don't like Eggers's playfulness (one of my co-workers said the title page was as far as he got into the book), but I think the 10-point sexuality scale of gay to straight is brilliant and just as important, to me, in choosing a book as the ISBN (i.e. who cares?). Here's half of the title page.
Contest time. Correctly identify the cover quirk on this Disney VHS cover (oops!) and I'll send you a Green Apple canvas tote bag. Email me to enter: pete at greenapplebooks dot com. I'll update this page when the prize is claimed. UPDATE: Prize claimed. There's a can't-miss phallic symbol in the dead center of the castle. Kudos to whatever artist snuck that one by Disney. Well played, I say.
By all means, share your favorite book cover quirks here, too. Play with us!