I'm incredibly interested in this as well. I found a thread with a AppleScript but it seems a bit out of date (
http://forums.omnigroup.com/showthread.php?t=10575 )
Looking at the Mail Rules, I wondered if something could be done with editing the header list, but to no avail. With gmail, for example, 'starred' items are stored (I believe) in a separate folder or given a label, and flags in Mail.app work in their own way, and a translation takes place. This would be different for other mail services and mail clients.
I'll keeping looking around.