It seems compiz has support for this. Under "General Options" in CompizConfig, on the "Display Settings" tab, it is possible to manually specify the "monitors" to use for maximizing windows. There is an issue with Adobe Flash and fullscreen, but overall it works quite well.

Since my graphics card merges three monitors into a single large one, this is very useful

Step by step instructions:

1. Open a terminal by pressing Ctrl+Alt+T.


2. Enter sudo apt-get install compizconfig-settings-manager and press enter. Fill out your password when requested. No asterisks will be displayed when entering the password.


3. When the installation is done, launch the application "CompizConfig Settings Manager".


4. Click "General Options" under the section "General".


5. Select the tab "Display Settings".


6. Uncheck "Detect Outputs".


7. Edit the list of outputs as desired. Each line is one monitor. The syntax is WIDTHxHEIGHT+X+Y.


8. See if works right away. You might need to log in and log out again.

Sample configuration for three classic 19-inch monitors in a horizontal row:

1280x1024+0+0

1280x1024+1280+0

1280x1024+2560+0