If it's not important to put a minimized window in the Dock, you can just hide the app instead. Command-H works in many apps; for the ones that don't, you can option-click on the Desktop if it's not full-screen, you can control-click on its Dock icon and choose "Hide" if you can see the Dock, and if you can't see the Dock, you can command-tab to the Finder where you can.
Hope that helps,
Charles