I loved Thunderbird in the beginning but I hate when a desktop application gets slow. After using it for more than a year, it became much slower than what I can tolerate so I've started to look around for solutions. I've found that it was slow because of the size of my mailboxes. First I took all my mails from the previous years and put them into seperate folders. It seemed it helped. But in fact it didn't.
Moving messages doesn't physically delete messages from the source folders. Because I receive a bunch of e-mails every day and I used to make daily backups of my inboxes (similarly to all other data files), I do care about the size of my mailboxes too.
Then I started to look for external solutions to physically purge my deleted mails. I couldn't believe Thunderbird lacks of such an important feature. Then Google enlightened me: it doesn't.
Compacting Folders. Remember these two words. :)