Manually Sort Folders
This extension for Thunderbird 3.0.1+ adds a "Manually sort folders" entry into the Tools menu. Use it to, hum, manually sort your folders (that was obvious, wasn't it?).
I sometimes put a development version online, but over the past two years, I've only updated this addon once, as it is very stable; so your best bet is to just stick with the publicly available version on AMO.