Harry Potter and the Methods of Rationality
Worm by Wildbow is also very much worth a try:
<a href="http://parahumans.wordpress.com/" rel="nofollow">http://parahumans.wordpress.com/</a><p>Not a fan fiction, like HPMoR, but rather a lengthy novel about superheroes and supervillains that takes the subject seriously and with an incredible amount of inventiveness. It may sound lame, but just try it for a chapter or two.