I've selected System -> Preferences -> Advanced Desktop Effects Settings
(I think it's available from a compizconfig-backend-gconf package; Otherwise, I 
guess e.g. gconf-editor can be used),
selected "General Options" and then unchecked "Unredirect Fullscreen Windows".
Afterwards I've re-enabled Compiz via System -> Preferences -> Appearance -> 
Visual Effects.
With EDuke32, icculus.org/duke3d and DOSBox, all running at the desktop 
resolution of 1280x1024, problem solved!

What I guess is that, assuming that option was enabled from the moment I 
install Hardy, it should maybe be disabled by default.
I say "maybe" because there could be other issues which I'm currently not aware 
of.

I could be wrong, but I guess that what this feature means is to render 
fullscreen apps on top of Compiz.
When it's disabled, OpenGL apps may bypass Compiz, which seems to work better 
for now. Again, I could be wrong here.

-- 
SDL applications auto-leave fullscreen if set to native 1280x1024 resolution 
and Compiz is enabled.
https://bugs.launchpad.net/bugs/216322
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