Disable window always-on-top

Yep, there's actually a program that does this, I just couldn't recall the name of it until now. It's called WinExplorer, by Nirsoft. It has an option, under the Size & Position tab, called "Set To No Topmost" that will remove the "always on top" flag from a window. It's an old app, but I'm still using it right now on Windows 7, to fix that annoying issue that crops up from time to time where sometimes windows will inadvertently get set as always on top after using "Show Desktop".

http://www.nirsoft.net/utils/winexp.html

This AutoIT script will let you manually set On Top for any open window: http://www.autoitscript.com/forum/topic/81398-window-manager-set-title-visibility-rename-etc-window-changing-stuff/

If you don't have AutoIT installed, a compiled version is here

I've created a small program that disables the Always On Top mode for all programs while it's running. If you open the program at startup and let it run in the background while you're using your computer, programs will never be in Always On Top mode.

You can download a ZIP file with the executable and the necessary DLLs here.

If you're interested in the source code, you can find it here.