Well, MS Office, iTunes, Quicktime, and others leave a cut-down version of the installer packages on the drive.
They then use these files as the location for the icon.
Although these files seem superfluous to requirements, and they are in the sense that some apps put nearly twice as much data on the drive than there apps actually require, the apps might start to throw up errors if they are absent..
The truth is, there could be up to 8 GB or so of such files on the drive and only a fragment of each one may be of any use, like a picture for an icon. Why iTunes can't include their icon in the main exe file I will never know.
In general, and to be sure, the programs you have with missing icons should be reinstalled in order to put the...