Robert's answer was spot-on. To expand on it a bit, and answer the OP's question about setting the mode en masse...
If you have a folder full of .exe files to process, you can do this:
for %x in ("*.exe") do reg.exe Add "HKCU\Software\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers" /v "%~fx" /d "WINXPSP3"
This example uses HKCU instead of HKLM; be sure to pick the one you really want.
To remove the settings, with a confirmation prompt for each one:
for %x in ("*.exe") do reg.exe Delete "HKCU\Software\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers" /v "%~fx"
Add /f
to the end if you don't want to be prompted for confirmation.
(If you vote this answer up, please vote up Robert's as well!)