Where did these missing OS X application icons go?
If restarting and all that doesn't help, here's how i fixed mine.


Open finder.
Go to /Applications.
Drag the offending application to the desktop to create a shortcut.
Shortcut should have the proper icon.
Right click shortcut and click on Get info.
Click on the icon on the top left of the info view. Example:


When icon is selected (blue highlight), hit Cmd+C to copy it. Example:


Delete shortcut (not necessary).
Go back to /Applications in finder.
Right click on the offending application.
Click Get info.
Notice the place where the icon should be Top left.
Click on that location to highlight it.
Press Cmd+V


You should now see your icon again.

Tip: This method can also be used to change any icon to something else and customise your Mac !