How to Hide Total Size and Free Space on Network Drives

If you're talking about laptops or desktops that are checked out/assigned to people, then simply do not give them administrator access. This will still allow them to install programs (Assuming they were written properly) to their home folder, and then when they leave, you need only delete their profile/user account to remove any programs they installed / changes they made. This will also limit the damage that a virus can do - simply quarantine & clean their documents on any system which they have not logged into, delete & recreate their account, restore their cleaned documents. Virus gone.

It's quite hard to actually create a "white list" of approved executables based on the fact that executable code need not even have a name, simply reside in memory on a page marked as executable. Your best bet is to simply make it easier for you to remove the unwanted applications when the user leaves.

If this is a security issue and not a "cleanup" issue, how did they get the programs onto the system in the first place?

You can not unless you have access to the Group Policies and can see which ones. Not every thing in the NETLOGON folder is executed.

To see what group policies (GPO) are being applied you can go Start, Run, CMD or WinKey+R and CMD and then type either gpresult on Windows XP or gpresult /r on Windows 7 and above. This does not tell you what scripts are being ran or what is actually in the group policies, just the ones being applied.

Also, since you are not the controller of the Group Policies, you shouldn't be the one troubleshooting it. Elevate it to the person that is in charge of that because you are wasting your time attempting to do it. Especially with little knowledge of how AD work.