I am a fan of 1632, the Dresden Files and Harry Potter fanfic. 1632 has its own website so no more about that here. The Dresden Files will be going on for quite a few more books and I'm a bit worried about what Jim Butcher will put Harry through before the end. Now that the Harry Potter series is all written, I'm happy to see all the good fanfic out there and at some point I may post my own.
If you are looking through my favorites, I do have a few unfinished stories in there but I try to only keep the ones that are really worth reading even though they are not finished. My favorite authors section should only have authors who are still posting. Not to worry, I don't just favorite every darned thing I come across, though it may look that way.
My very favorite stories, to be reread again and again:
End Of the Line id:3673824 The afterlife, for various Harry Potter characters, xover with Discworld
Pet Peeves: Harry Potter
Gringotts Bank: The author has some character go to Gringotts and prove that he/she is the long lost sister/brother/cousin of so&so, the goblins allow access to the vaults and they clean them out. Um, this is a bank, their job is to protect their clients money! Even if the owner of the vault is dead, the bankers are going to fight legally, illegally, possibly physically and magically to keep things the way they are. Make your characters work for that treasure.
Also, Gringotts is a bank, not a legal court, a dating service, a school, or any other weird thing you want it to be. If you want your characters to be emancipated, forced into marriage, trained at war, given special powers, and so on, make them work for it! At least have them work at getting along with goblin characters to gain that special goblin knowledge, and by work I mean work harder than showing up at a counter and saying, "Hi Griphook!" and Griphook is all "No Human has remembered my name before! Sob Sob Now I will give you the keys to the kingdom!"
New update 3/18/12:
Character bashing: I get that you hate Ron, Molly, Snape, Mrs. Figg, whoever. I don't actually mind if you write them to be evil scum or brain-dead zombies or whatever, JKR left a lot of room to write most of her characters whatever way you want. However, I find it a bit tedious to read a story where Snape spouts a few evil things, is hit by an anvil, staggers off, spouts a few more evil things, is dumped into the castle cesspool, crawls out, rinse, repeat at least 3 more times. It would be nice if you would put a disclaimer in the appropriate chapter(s) saying "Just going to torture a character for a few thousand words this chapter, no plot or anything, feel free to skip to the next chapter".
To make it clear, I'm complaining about the actual mind-numbing grinding to halt of a story for the purposes of torturing a character, here. If your version of character X could plausibly have done at least 60 % of what he was supposed to do in canon, feel free to say that he tortured babies / sold dorm-room pics of Harry to support his Chocolate Frog habit / and was personally responsible for confunding at least 10 characters to act like idiots in his spare time. That said, fit the geek into a story, please.
Another suggestion: If you are writing a longer story and can foresee posting new material for a year or more, consider using descriptive chapter titles. When your readers come back to your story, vaguely remember it, and want to check if X happened the way they remembered, chapter titles will help them skim through the story rather than rereading the whole thing.
Yet another suggestion: for those who can't figure out apostrophes, an apostrophe s either replaces the word 'is' or shows ownership. So if your word cannot be changed into 'so-and-so is' or 'so-and-so owns the' don't use the apostrophe.
Word choice: Accept/except : accept gathers someone/something in, I accepted a present. Except singles something out: They all got presents except him. Remember except is about an exception to the group.