Since still people didn't get it:
What to do:
1) Start i.e. warcraft3 in wine with your full desktop resolution (I have set a virtual desktop for handling applications like a normal window).
2) Press alt+tab
-> After a short flicker another application will have the keyboard focus, but warcraft3 will still be in the foreground.
3) Change your workspace with i.e. ctrl+alt+right. warcraft3 will after a short flicker be displayed on this workspace in the front of all windows too.
4) Try minimizing it with the "show desktop" function of the window manager. After a short flicker your window manager thinks warcraft3 is minimized, but it is still displayed fullscreen on all workspaces.
With catalyst 10.10 no window can be put in front of a big window with 3d-content.
In earlier versions of catalyst it sometimes worked, as long as the window you wanted to place over it was not maximized or bigger as the desktop resolution. But sometimes it didn't work and sometimes X just froze.
Putting windows above 3d-fullscreen windows works with the proprietary nvidia driver, with xf86-video-ati and I think it also works with xf86-video-intel.
Someone in the archlinux irc suggested that it is because fglrx doesn't use dri2 properly but rather something like dri2.
From my Xorg.0.log I see
So maybe he is right and the dri implementation of ATI is more dri-like instead of dri2-like.
[ 24578.166] (II) Loading extension ATIFGLRXDRI
[ 24578.309] (II) AIGLX: Loaded and initialized /usr/lib/dri/fglrx_dri.so
It also says
but that doesn't mean, that it is used, right?
[ 24576.794] (II) "dri" will be loaded by default.
[ 24576.794] (II) "dri2" will be loaded by default.