Mac App Store - While downloading a new app, the icon transparency changes according to the progress of the download.
/via Florent Gosselin
Adium- The eyes of the bird icon open while using Adium and close when you close the app.
/via Bartosz Hernas
Windows 7 - Hover colors of dock buttons change according to colors of app icons.
More information here:
Mac App Store - The progress bar of installing an app from the Mac App Store changes its dimension separate from the icon, when magnified in the dock.
Reeder - Dock icon with unread items indicator upgrade