Today I decided enough is enough. After a brief Google search I found the solution to setting the reply position on e-mails to the top instead of the bottom. The stupid thing is that it's not an application-wide setting, it's an account setting.
1. In Thunderbird: Go to "Edit > Account Settings" *
2. Select "Composition & Addressing" for the account in question
3. Make sure the "Automatically quote the original message when replying" checkbox is checked.
4. In the dropdown box below that, select the option "start my reply above the quote"
This worked for Thunderbird 1.5, ymmv
If you found this advice helpful, please consider making a small donation to The Mozilla Foundation, the non-profit group that brought us Thunderbird.
* update: on Windows, the option can be found in: Tools -> Account Settings.
update 2: If you're commenting to say "thank you": You're welcome!