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Note: Here we describe a workaround. The proper solution is to fix the graphics drivers and the X.Org X server. Such work is taking place, and for several cases you do not need this workaround. Especially with newer versions of Linux.

You just installed your 3D Linux desktop and you are really enthusiastic about it. But when you try to play some videos, you get a strange black output. What’s going on?
The common software video players that come with the Linux desktop are able to display the video stream to several types of output devices. This includes several types of output for the graphical interface, and also obscure output devices such as text mode, using ASCII characters.
The default output device is XVideo (or Xv) for players such as those based on GStreamer (totem) and VLC.
As you guessed, there is a bug with XVideo when using Beryl/Compiz. Therefore, to fix, you need to switch to another output device that works.
For GStreamer players (such as totem, the default movie player in GNOME, Ubuntu and so on), you need to run from the command line the command
gstreamer-properties
(with older distributions such as Ubuntu 6.06 there is an option in System/Preferences for this).
and pick
Video, then for Default Video Plugin choose X Window System (No Xv). Click on test to verify that it actually works. Click Close and you are set.
VLC is not installed by default in Ubuntu 6.10. You need to install manually using the Synaptic Package Manager (under System/Administration), once you have activated the Universe repository in Repositories.
Start VLC and click on Settings, then Preferences. Expand Video and then expand Output modules. You will notice several options for output device. How do we actually choose which one should be the active output device? Well, it appears it’s a bit tricky. Select the item Output modules, and notice the checkbox at the bottom right that says Advanced options. Check the box, and now you have the option to select a different output device. Pick X11 video output, click on Save and you are set!

Update (17 Jun 2007): Added section at UbuntuGuide.org, How do I fix black windows during video playback.