Hiding an Active Application's Dock Icon
You can remove an active application’s icon from the Dock manually, with a very simple .plist trick.
Hold down the Control key and click on the applications’s icon in the Finder. Choose Show Package Contents from the menu. Open the Contents folder, and then open the Info.plist file. At the bottom of Info.plist, change:
<key>LSUIElement</key>
<string>0</string>
to:
<key>LSUIElement</key>
<string>1</string>
Then save the Info.plist file and relaunch the application. If, after the relaunch, it continues to show up, open the terminal and run the touch command. As an example, here’s how to touch BBAutoComplete.app:
touch /Applications/BBAutoComplete.app
To make the applicaton’s Dock icon visible again, change the Info.plist file back; that is, change the 1 back to a 0.
Credit: I originally found this little trick in the BBAutoComplete manual, and the touch command from the MacOSXHints web site.