I once wrote an windows (mfc) application that minimized to the system tray. There are a few MFC classes around that offer this functionality, have a look on developer.com you should be able to source some stuff there.
Maybe you could do a shell call to your perl program and let the MFC classes handle the windows side of things.
I haven't used Perl TK stuff yet, this could possibly allow you the same functionality as MFC. Maybe some other monks with TK experience can help you out here..

Jorg

"Do or do not, there is no try" -- Yoda