I use Mozilla Thunderbird as my email client. Overall, it works well, but there have been issues, probably because I never seem to delete anything.
5/27/2010 I had a problem with the index being out of sync with the messages in the inbox, so when I clicked on a subject, the message was not necessarily the right one, and some of the messages displayed wrong, like showing html in source form. With a little research, I found this article about compacting folders that explained a lot about Thunderbird files. There are strategies there for solving several problems, and what worked for me was exiting Thunderbird, going to the thunderbird profile C:\Users\eburdick\AppData\Roaming\Thunderbird\Profiles\i0lcy4dt.default\Mail\mail.edburdick.net and deleting all of the *.msf files. When I restarted Thunderbird, it recreated the files from the messages and things seem back to normal. This has happened again multiple times, and the same strategy seemed to help. I do find that if I keep the inbox from getting too big (and mine tends to get very big) the problem happens much less often.