I ran into an issue with Thunderbird eating up a ton of disk space when run for a long amount of time. My dad first experienced this issue when he tried to check his e-mail and it said his Inbox was full. There was tons of space though. I checked the Application Data for Thunderbird on his account and then realized that the Inbox and Trash directories were eating up 2 gigs of space. But the folders were only using about 2 megs total. After some research I found out that when you delete or move e-mail messages it doesn’t remove them from the folders, it just marks them as deleted and doesn’t free the space. So to clear up these large files, the boxes need to be ‘Compacted’. This removes all the messages that were previously deleted and frees up the space. This can be done by right clicking on the folder in question and clicking ‘Compact’. It works for Thunderbird 2, all versions. I’ve posted an attachment in case you have any questions.
Just posting this here in case someone runs into a similar issue.