If you use a repackaging tool that performs "before" and "after" snapshots to build installs, here is a way you can make package cleanups faster and easier: Start your "before" snapshot after the software you are repackaging has completed its "pre-install" routine.
Example: This is a good technique to use with software that was originally authored in InstallShield Wizard format. Execute the installation right up to the point where InstallShield says "setup has enough information to begin installing". Perform your "before snapshot", then complete the installation.
If do you use this technique, be aware that some pre-install routines create required registry entries that contain product keys. Several Adobe and Macromedia products do this. However, they can easily be re-imported into your package. There are also several entries in the AppDeploy Package Knowledge Base that discuss this.
The advantage of this is that many registry keys, files, and folders that are used by legacy setups but are not needed for the software to function are not captured and can't become part of your package. You spend less time cleaning, and finish with a smaller, uncluttered installation.