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Personally I'd put it to web animation folder.
From what I could see, usually under "Fan Works" go mostly Fanfics, while other kinds of fan works are put under the kind of work they are (in this case Web Animation).
What they said; Fan Works is mostly fanfics, abridged series, and other fan works you're unsure where to place. If the fan work has another definite medium, it can go in its dedicated folder.
The one folder fan works should never go to is "Web Original" since they are, by definition, not original.
^ There are many here who interpret it as "works original to the Web", not "Web works which are original".
I had a dog-themed avatar before it was cool.
^ Is that not what Web Original means?
Currently Working On: Incorruptible Pure Pureness
OK, I just created the page for Star Trek Logical Thinking and, like any good troper, I want to cross-wick it. For newbies, that basically means, I want to put the examples on their trope pages. Trouble— does it belong in Fan Works (because it's based on Star Trek) or Web Animation (because it was animated on the Internet)?