Horn Book put out a bunch of "Best of" lists, including this one, for YAs.
NPR's got a Three Books for the Smartest Teens You Know list*.
Reading Rant's Ten Most Underappreciated Teen Books of 2000-2009.
Amazon's strictly-by-the-numbers Best Books of 2009.
Bookalicio.us has a Top Fifteen list (because ten just wasn't enough!)
And I'm sure there are more that I just haven't seen yet! If I missed a list you've seen, note it in the comments.
Most surprising to me is that Justine Larbalestier's Liar wasn't on any of the lists I've seen. I know it was one of those books that you either loved or hated (I loved), but I thought I'd see it pop up on at least one list. Perhaps the cover controversy overshadowed the book itself. Unfortunate, because if I did have a top ten list, I'm pretty sure I'd put Liar on it.
UPDATE: Just saw the Kirkus list, and they've included Liar and a whole bunch of the Cybils Nonfiction Middle Grade/Young Adult nominees as well!
*Haven't read a single one. Oops.
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