Quick notes: I'm not personally fond of large stretches of verdana; it's a very light font that tends to mush into visual fuzz on the screen. It's very *pretty*, but pretty doesn't equal reader-friendly; if I had a primary critique of the entire site design it would be that it is designed more to look elegant in screen shots and printed out that it is to be comfortable for long periods of reading.
And while my Verdana-dislike may be to some degree personal for general use, it is unambiguously awful for huge uninterrupted lists such as the Yuletide fandom list. Other design flaws: if a person follows the natural flow of reading they end up paging up and down constantly to find the fandom they are looking for, and the page has no visual rhythm whatsoever. My immediate quick fix would be to reorientate right to left, break up by letter and put in a large intermediary letter to both allow a reader to swiftly zero in on their search area and to break up the page more. This of course, in a dynamicly generated system, leads to the problem that it will look wrong for collections that don't feature so many fandoms. Which is an example of what I would call the primary structural problem: what is an adequate site design for individual authors is a dreadfully illfitting one for collections and archives. One size don't fit all.
What is however worse is _you can't find it_; the fandom list is likely the page the majority of casual readers want to navigate from, and it's obscured. I had no idea it was there until someone pointed it out, and I had no reason to know. Not only because it is sitting up on the system menu rather than down with the Yuletide information, but I have used AO3 before for individual users and that tab leads to the entire AO3 collection of fandoms. A system menu should change very little across the entire site, and when it does it should be immediately obvious that a new tab/destination is in. On top of that, when the reader finishes their first story, flush with the victory of having found a way to navigate Yuletide, and clicks on that very same tab from the story page, they will be dumped into the overall site fandom list instead. And having Yuletide story pages use that tab to go to the collection list screws up people who are reading by author not collection. It's just bad, bad design.
Having the actual Yuletide 2009 links leading to the 'About' page is also bad design. I spent several cycles of clicking on various Yuletide links and not finding any actual stories before determining that it was not the large and obvious "Yuletide" and "Yuletide 09" links that would lead me to stories, but the tiny bland number link off to the bottom and right. People mostly don't want to read you going blahblahblah about Yuletide; they want to go straight to the stories. The most obvious link should lead to the primary interest.
Really, it shouldn't even lead to the stories+filter page, given the uselessness of said page for filtering; it should lead to the fandom list page, which of course brings up issues of consistency. When you have to break consistency to make your links usable to readers, it's usually a good idea to rethink your basic design. The narrow right hand box may look pretty, and it may have seemed an elegant way to keep the filter choices and stories on one page when testing with small groups of stories, but it scales very badly. Even for individual authors, it quickly becomes awkward if they work in a lot of fandoms and characters.
I'm not sure how I would have designed it; given that the pages are dynamically generated, I might have thought about a tab paradigm, where you can click back and forth between a large comfortable search page and a story list generated by said search page. But it's been years since I designed web pages, so I'm not up to date on best practices thinking.
There's probably lots of stuff I missed, but that's my thoughts from a quick once-over.
(For the puzzled, AO3 is Archive of Our Own.)
ETA: actually, I should say that I don't really mind Verdana at smaller font sizes, it's when you go up in points that the lightness comes out for me and it starts to mush. It's still crap for an undifferentiated list, though it's not like anything is really good. it's like text without paragraphs... visual rhythm!