By modifying this small setting, you can make the Dock show which applications are hidden by displaying them as a semi-transparent icon. To do this, open up the Terminal (Applications/Utilities) and type the following:
defaults write com.apple.Dock showhidden -bool yes
For this change to take place, you have to relaunch the Dock, using Activity Monitor. Do this by loading up Activity Monitor (Applications/Utilities) and typing dock into the search field. Quit the process named dock.
To cancel this change, and return the icons to normal, repeat the above command in the terminal, but replace yes with no.