How to make hidden application icons transparent on Mac OS X
In Mac OS X, clicking on the red button in an application's titlebar or clicking on the application's name in the menubar and choosing "Hide {APPLICATIONNAME}" will hide it from view until you click on its icon in the Dock.
By default the icons for hidden applications look no different than those for visible applications, but you can change this setting using the command below.
To make the icons for hidden applications appear transparent in the Dock, open a new Terminal window and enter these commands:
defaults write com.apple.Dock showhidden -bool YES
killall Dock
To revert the change, open a new Terminal window and enter these commands:
defaults write com.apple.Dock showhidden -bool NO
killall Dock