In this page we are trying to give some answer to problem that have been brought to our attention but which do not depend on guake iself.

gnome-panel stays on top of Guake when using Compiz

Using compiz you might encounter this instead of this.

In this case you might want to do:

Open Compiz Config Settings Manager and enable Place Windows. Then, on Fixed Window Placement tab, add a line in Windows with fixed positions with

 Positioned windows: class=Guake.py
 X Positions: 0
 Y Positions: 0

(Thanks to Liquen for the solution)