Harry Potter

Bella_Centric - An LJ Community devoted entirely to fanfiction which - surprisingly enough - is centered around Bellatrix Lestrange.
Betrayal - This LJ community dedicated to the Voldemort/Hermione pairing has been going for nearly 4 years now, and features fandom and pairing discussions, as well as regular fanwork postings.
Dystopia - Home to perhaps the largest array of Tom Riddle fanfiction on the Internet, and a selection of interesting essays on the character.  Also home to the Guilt by Association webring, for Voldemort/Death Eater supporters.
GT: Reloaded - A post-Deathly Hallows resurrection of the fabled Gryffindor Tower - the original Harry/Ginny site that was responsible for bringing the GTDEs together. Contains forums, fiction archives, and undoubtedly more to come.
Half-Blood Prince - Facts and opinions about the ever-quotable Professor Severus Snape, including links to a small collection of fanwork.
Ink - A Harry Potter fanfiction site orientated around the dark families of the Potterverse, including Severus Snape, Draco Malfoy, Lord Voldemort and many others. Apparently, they're of the opinion that the Dark Side is sexy...
Slytherins.com - A huge site dedicated to the House of Slytherin, with forums, fanwork, and fanlistings for many prominent house members.
Tom-Riddle.org - The official fanlistings.org-supported fanlisting for Tom Riddle/Lord Voldemort. Featuring over 1,000 members at our last update!

Heroes

Burnt Toast Diner - Famous for its waffles, and for being the place where Heroes fans come for coffee, love and murder.  
HeroesBoard.com - A popular and active unofficial forum dedicated to the discussion of NBC's TV show Heroes.

Supernatural

Supernaturalville - Home of the Supernatural Virtual Seasons, this site aims to promote high quality, original fanfiction for the show, and also contains a discussion forum. 
Supernatural.tv - Featuring an Episode Guide, Image Gallery, and a variety of fanfiction and fanart.