For those of you experiencing
slowdowns on Mac OS’s Mail application over some time, this might
be a cheap trick for you to get back speed and disk-space.
Mail, is keeping track of mail message subjects in a database, to
quickly scan, search and organize threading in your
mailboxes.The good thing is: once you delete a mail, it is also gets deleted
in the database…
The bad thing is: a database needs to be maintained, and this is
not done automatically…

What does this mean now….
…your database deletes items by reference, but it does not free
up the allocated disk-space, thus blowing up your overall database
size which leads to longer access times as more (empty) data needs
to be parsed through.

The solution:

While your Mail application is NOT running…
…use a terminal and go into “cd ~/Library/Mail”…
…open the database with: “sqlite3 Envelope Index”…
…and free up the already deleted database disk-space using:
“vacuum subjects;”…
…et voila, quit sqlite3 and you’re done.

Mail will be quite fast again, and your disk capacity should show a
few more free blocks.