SemTop! is a nifty tool that allows to keep important windows always on top of the desktop and doesn't allow other windows to overlap it.
The software resides in the tray area as "drawing-pin" icon and allows
to "pin" necessary windows with single mouse click. Just press mouse
button on tray icon and drag the "pin" cursor to window which you would
like to keep on top or return to previous state.
Alternatively you can just press some hot-key (which can be specified in
the program settings) when the window are active.
Function auto-on-top allows to set some application windows permanent top most status,
which activates automatically every time when it starts.