Thanks for the idea; I also pretty much only use X11 for Matlab, and am happy to reclaim the Dock space.
1. Open /Applications/X11.app
2. Right-click, Show Package Contents
3. Open Contents
4. Open Info.plist in your text editor of choice, or Property List Editor if you have DevTools installed.
5. In the main <dict> section (say, below CFBundleDevelopmentRegion) add the following:
Code:
<key>NSUIElement</key>
<string>1</string>
6. Save.
7.
Very important: Drag X11.app onto your Desktop. OS 10.3 caches Info.plist files, so your change won't get noticed right away otherwise.
8. Double-click and enjoy the silence in the dock.
9. Move X11.app back to /Applications.