SemTop! is a nifty tool that allows to keep selected 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.