AppTrayer lets you minimize any application that you start with AppTrayer to the system tray.
The application is not capable of putting already running applications in the system tray.
Minimizing a long running python script to the system tray with a custom icon:
apptrayer.exe --icon=C:\path\to\icon.ico "C:\python26\python.exe" "C:\path to\my\script.py"
--icon=<path> Show a custom icon instead of the application icon. --minimize Start the application minimzed.