Having dug into this a little, I can confirm that when the new Mail.app converted my existing cached IMAP folders to the new format, it left the old messages in place. For example, I have a folder called CoolTech which has 4281 messages totalling 18.1MB. (I got this from the cool new Account Info window in Mail.app.) If I drill down into ~/Library/Mail/IMAPxxx/AAtech/CoolTech.imapmbox I can see two subdirectories: CachedMessages and Messages. Each contains about 4,300 files. (Remember: I've been receiving new messages and deleting some since I did the Tiger upgrade.)
So we've established that upgrading to Tiger will double your on-disk mailbox usage - at least, if you're an IMAP user: I don't know about POP. The question is, how to clean up? How about the Rebuild command? The Help describes it thus:
For IMAP accounts, the table of contents file is moved aside, and locally cached messages are also discarded. All the messages are retrieved again from the server to your hard disk and the table of contents file is rebuilt from the newly downloaded messages and from data in the old table of contents file.
So let's go ahead and try it.... [long pause with lots of network and disk activity] No, it doesn't work. Or rather, it works exactly as advertised: all of the message files in the new Messages subdirectory were refreshed, but the old CachedMessages directory was left untouched.
Obviously I know how to walk the tree deleting the old stuff (using find in a Terminal window), but it's odd that Apple didn't provide for this.