There was just one floppy, the first issue of DC's for-lifelong-readers-only crossover event Final Crisis, with the Dark Knight in it to crack the top 10. All the other 9 monthly comics were from Marvel (with 8 of them coming that company's only slightly more accessible crossover event, Secret Invasion).
In the hardcovers and paperbacks*, however, DC dominated. No Marvel publication cracked the top ten. The top spot was held by Watchmen, capitalizing on buzz from the upcoming movie adaptation, and three of the next five were Batman titles, The Killing Joke**, The Joker, and Batman: The Dark Knight Returns. All three are excellent, as are the other ones on the list (though of course if you want to pick up The Walking Dead or Fables, you should start at the beginning).
* - I hate that they call them graphic novels. It always makes it sound like people are afraid to admit to reading comics but "graphic novels" sounds snooty enough to be acceptable. But a graphic novel is a specific thing, not just comics bound like a regular book.
** - Instead of the standalone Killing Joke, I'd suggest DC Universe: The Stories of Alan Moore, which collects The Killing Joke, two of the best Superman stories ever, a decent Green Lantern one, an ok Batman one featuring Clayface, and some other stuff that I don't really like. But it costs about the same as the Killing Joke by itself, so if you find anything else in it mildly entertaining, you're better off with this one.
After The Scarecrow, Ra's Al Ghul, The Joker, and Two-Face, who should be Batman's next enemy in the Batman Begins/The Dark Knight series? Well, as of now we know that Tom Hardy will play Bane and Anne Hathaway will play Catwoman.
Check out the master list for all the villains covered. I've pretty much run out by now. Obviously, there are more Batman villains, but not any of significance that I know of. As of February 2009, no one is confirmed as a villain. Not the Johnny Depp Riddler, not Phillip Seymour Hoffman Penguin, nobody.