Apple - Where did these missing OS X application icons go?

If restarting and all that doesn't help, here's how i fixed mine.

1. Open finder.
2. Go to /Applications.
3. Drag the offending application to the desktop to create a shortcut.
4. Shortcut should have the proper icon.
5. Right click shortcut and click on Get info.

6. Click on the icon on the top left of the info view. Example:

   

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

   

8. Delete shortcut (not necessary).

9. Go back to /Applications in finder.
10. Right click on the offending application.
11. Click Get info.
12. Notice the place where the icon should be Top left.
13. Click on that location to highlight it.
14. 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 !

For me, the problem was with Terminal.app. It was an app I had set to "Keep in dock". What happened was the icon for Terminal.app started displaying on the dock and in the Cmd-Tab panel as the default icon:

What I had to do to get the original icon back was, while the app was opened, right click on the dock icon and select "Options -> Keep in Dock" and remove the checkmark, then I followed the same procedure selecting "Keep in Dock" again to get the checkmark back.

After that, I got the familiar Terminal icon back.