PCA is intended to detect issues with older programs and not intended to monitor programs developed for Windows Vista and Windows Server 2008. The best option to exclude a program from PCA is to include, with the program, an application manifest with run level (either Administrator or as limited users) marking for UAC. This marking means the program is tested to work under UAC (and Windows Vista and Windows Server 2008). PCA checks for this manifest and will exclude the program. This process applies for both installer and regular programs.
Another option to exclude applications from PCA is to add the list of executable files with full path under the following registry key: HKEY_LOCAL_MACHINE\ Software\Microsoft\Windows NT\CurrentVersion\Compatibility Assistant. The value name is ExecutablesToExclude, which is type REG_MULTI_SZ.
PCA automatically excludes programs running from network locations and programs containing fixes applied to them in the application compatibility databases.
A group policy setting is provided to disable PCA for all programs if desired. The name of the policy is Turn Off Program Compatibility Assistant. It can be found under Administrative Templates\Windows Components\Application Compatibility in the group policy editor (gpedit.msc).
There are also individual policies to turn off specific scenarios. These policies are available under Administrative Templates\System\Troubleshooting and Diagnostics\Application Compatibility Diagnostics in the group policy editor.
PCA automatically excludes programs running from network locations and programs containing fixes applied to them in the application compatibility databases. But the shim infrastructure will still be loaded in the process space even when the application is excluded from PCA.