Apple-loving weblog TUAW highlights a simple Terminal tweak that makes all of your hidden applications appear translucent in the Dock. Just fire up Terminal and paste:
Then restart the Dock by pasting
killall Dock and hitting enter. Once it restarts, any app you hide shows up dimmed in the Dock. You can make this tweak along with many others with previously mentioned Secrets, but if you'd prefer not to install another preference pane, this Terminal tweak will do the job.