My favorite story in HP is Underwater Light--still a WiP but apparently is going to finish up in July. I've been following this for two years. It's fantastic.

http://www.schnoogle.com/authors/maya/UL01.html

Other favorites:
http://www.skyehawke.com/archive/story.php?no=2226
http://www.rebeccalizard.net/nlts/stories/invisibletosee.html
http://yearningvoid.net/julad/lustre.html
http://daisygrrl.com/quidditch/quidditch01.shtml (OMG. Funniest. Story. Of. All. Time.)
http://bloom.velveteen.net/four.html

My favorite fucked-up Harry fic: http://www.thedarkarts.org/restrictedsection/fic.php?fic=tda:/authors/maya/YEW.html