I've just noticed that the Thunderbird email client doesn't need to show all the special folders (e.g. sent, drafts, templates) in an account. Google couldn't help me find out how to get rid of them, so here's what I found out (without google's help).
It wasn't too easy to do because there's no option to delete a special folder within the Thunderbird UI (I'm currently using version 2.0.0.12). But it turns out that there's nothing fancy; nothing to do with prefs.js, nor the registry. I spent a while looking through both before it occurred to me to look at the file structure of the account directories.
Before continuing, please note that the following instructions worked for me. They may NOT work for you, and may even damage your computer. Do not continue if you don't understand what you'll be doing!
First, shut down Thunderbird so that it doesn't get confused when we delete files from under it.
Find where Thunderbird stores your mail. Mine is relocated because I've migrated my mailboxes from another computer, but by default on Windows, it should be in "C:\Documents and Settings\samson\Application Data\Thunderbird" ("Application Data" is a hidden folder). You'll need to change "samson" to your own account name, of course.
Within the Thunderbird application data directory, there should be a "profiles" directory, and if you continue down the tree to "Default User", you should find another directory with a random name. This is your profile within Thunderbird (where it stores your mail). If there are more than one, you'll have to figure out which is the one you're actually using.
At this point, you may want to make a backup copy of your Thunderbird profile. If anything goes wrong, you can overwrite your profile from your backup copy, and everything should be as it was before you changed anything.
Continue down to the "Mail" directory, and you should get more directories named in a similar way to your Thunderbird accounts. Go into the one you're interested in and notice that there are some 0-byte files there. The ones that you may be interested in are "Drafts", "Templates", and "Sent"; each one with no filename extension.
Finally, delete the 0-byte filename corresponding to the folder that you want to delete within your account within Thunderbird. Repeat as desired for other your other account directories, and restart Thunderbird when you're done.