I want to use Mailbox Manager to set a server-side rule or schedule to empty Microsoft Office Outlook 2003's Junk E-mail folder, but I can't figure out how to do so. Can you help?

I took your question to Exchange MVP Todd Booher, who told me that Mailbox Manager can do what you want, just not by default. You have to add the Junk E-mail folder as a custom folder type, then tell Mailbox Manager to permanently delete items in that folder, according to the schedule you set.