Yeah, I'm all over "The Doom that Came to Gotham". Mignola is always a winner, of course, but I love their take on his rogue's gallery.
Don't forget the classic "Gotham by Gaslight", either. Kicked off the whole Elseworlds craze back then. "Holy Terror" was also an interesting read, with the Batman mythos set in a theocratic Cromwell-ian commonwealth.
I also dig "Arkham Asylum" with writing by Grant Morrison and art by Dave McKean. *Very* adult look at the villains, with surreal art and an almost-mythic tale around it.
"Red Rain" was a cute idea, but IMHO, they went too far with it.
There's also the Frankenstein homage, "Castle of the Bat", but it's best avoided, much like the Houdini crossover (yes, really.)