This application will attach itself to one of your windows and automatically make all minimize actions go to the system tray. Also gives you some extra control over the window, including a more advanced implementation of Always On Top and alpha transparency. Also monitors whether the process has stopped responding, and puts an End Task option on the right-click menu if it has. Unfortunately, the same menu bug exists here as in Always On Top (if you open the menu, you cannot close it without choosing one of the options).
Application (32-Bit Windows)
Sorry, no source. This contains some code for another project I am developing to make Windows programming much easier, and I'd prefer if it didn't get released yet.