As a general rule, I usually exclude anything that does not appear to be neccessary for the application to function or that may have been captured during a reboot or other process not related to the app.
Without knowing what, specifically you are trying to capture it's hard for me to tell, but my guess is if it's not an application that needs specific security policies or permissions, I would exclude them.
Look up Security Configuration Files in the MSDN for more info on these types of files.
