That was easy enough to solve: my software wasn't handing not-found pages correctly; it was aware that the files weren't there, it just wasn't bothering to send back the proper response to the webserver. I hadn't bothered to actually write that part of the code.
I fixed the problem (although the error pages themselves are rather spartan) and then spent some time going through the error log seeing what problems I could fix. One typo on the template page probably accounted for half the failed requests; the rest were typos in individual entries and missing files from way back. For instance, an entry over two years ago when I was still playing around with formating entries. It pointed to some mockups I had done that I had neglected to actually copy over when I went live. It's interesting to look at those mockups and compare the format I'm using today (which just revealved another display bug that I'll need to get around fixing. Sigh). I actually liked the rounded corners I used originally but I used a hack to get them and (as the sidebar on those pages show) they don't always work like I intended them to, which is why I dropped the concept.
I eventually solved the problem I was having with Lynx by using CSS and because of the loss of historical context for that entry, the opening sentance now makes absolutely no sense whatsoever. Of course this is the layout you are looking at right now.