Thunderbird: auto delete duplicate messages
Released by Thorsten W. Schmidt on the Mozilla site, the add-on searches a given folder for duplicate messages and automatically deletes them by tagging all duplicates with a delete flag and one message with the keep flag. To use it, first install it from the Mozilla site. Once installed, open Thunderbird and right click on a folder. Click "Remove Duplicate Messages" and that's it.
The add-on also lets you configure what fields you want to compare such as sender, message, etc. It also checks sub-folders, and can analyze about 1000 messages per second. Finally, you can choose to keep the the bigger, smaller, unread, first found, or last found Message if you have a preference.