After recalling Henri Svinonen's pesterings about data, I decided to see the suitability of my dataset for this task. For data management reasons, I only grabbed the data from the second half of the year (about 10 million messages). I know from memory that the quality of Python's message parser (which was used to extract data in the first place) is surprisingly poor, which introduces bias of unknown consequence to my data. Since I only extracted headers, I can't identify charsets for anything which was sent as, say, multipart/alternative (which is more common than you'd think), which introduces further systematic bias. The end result is approximately 9.6M messages that I could extract charsets from and thence do further research.
Discussions revealed one particularly surprising tidbit of information. The most popular charset not accounted for by the Encoding specification was IBM437. Henri Sivonen speculated that the cause was some crufty old NNTP client on Windows using that encoding, so I endeavored to build a correlation database to check that assumption. Using the wonderful magic of d3, I produced a heatmap comparing distributions of charsets among various user agents. Details about the visualization may be found on that page, but it does refute Henri's claim when you dig into the data (it appears to be caused by specific BBS-to-news gateways, and is mostly localized in particular BBS newsgroups).
Also found on that page are some fun discoveries of just what kind of crap people try to pass off as valid headers. Some of those User-Agents are clearly spoofs (Outlook Express and family used the X-Newsreader header, not the User-Agent header). There also appears to be a fair amount of mojibake in headers (one of them appeared to be venerable double mojibake). The charsets also have some interesting labels to them: the "big5\n" and the "(null)" illustrate that some people don't double check their code very well, and not shown are the 5 examples of people who think charset names have spaces in them. A few people appear to have mixed up POSIX locales with charsets as well.