Can Apple Mail be optimized to perform well when I have 30k messages in my inboxes?
The easiest thing to do is clean up the index file Mail uses to track the messages:

  sqlite3 ~/Library/Mail/V2/MailData/Envelope\ Index vacuum;


Thanks for this tip to the estimable Brett Terpstra. The linked article explains how to make an AppleScript file to measure things before and after to see if the operation thinned out the size of the file Mail uses to store the pointers to the messages. I would add, quit Mail and make a backup before trying to clean the file. A vacuum operation is normally harmless, but why not get a backup just in case.

Also, this thread probably goes back to @bbum and his weblog-o-mat and perhaps even deeper back...