There are many fanfiction sites that are not fanfiction-dot-net,
however, they are going to be the larger fandoms such as Twilight,
Harry Potter, Star Trek, and such. Most of the smaller fandoms like
manga and lesser-known books and shows, are just going to have a
few fanfiction stories and those will most likely be on
fanfiction-dot-net.
Type "___ fanfiction" into your search engine, where the blank
is the type of fiction you're looking for, and it will show
whatever's out there.
You might also try LiveJournal and search for communities that
feature fanfiction.