I've read that gnome shell + mutter is supposed to detect fullscreen and then unshape the viewing area, removing all window manager dooads, and increasing performence in classic fullscreen mode while not sacrificing usability (fullscreen panels: bad; windowed panels: good).
This doesn't work. Just install dosbox in ubuntu and press alt+enter and you will see the ugly truth - upper panel not removed, though the hotspot and other functions are disabled. (though you might have to try more than once; once in a blue moon it works. Exult doesn't though).
ProblemType: Bug
DistroRelease: Ubuntu 12.10
Package: gnome-shell 3.6.2-0ubuntu0.2
ProcVersionSignature: Ubuntu 3.5.0-20.31-generic 3.5.7.1
Uname: Linux 3.5.0-20-generic x86_64
NonfreeKernelModules: fglrx
ApportVersion: 2.6.1-0ubuntu9
Architecture: amd64
Date: Mon Dec 10 12:53:28 2012
DisplayManager: lightdm
GsettingsChanges:
InstallationDate: Installed on 2011-12-25 (350 days ago)
InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release amd64 (20111012)
MarkForUpload: True
ProcEnviron:
TERM=xterm
PATH=(custom, no user)
XDG_RUNTIME_DIR=<set>
LANG=en_US.UTF-8
SHELL=/bin/bash
SourcePackage: gnome-shell
UpgradeStatus: Upgraded to quantal on 2012-10-20 (51 days ago)
This occurs in a fresh Fedora install too. I've managed to recreate the bug in VLC, various games, Minecraft and Adobe Flash Player. Unlike the bug reports similar to this one, this bug has nothing to do with Compiz.