Here are 2 suggestions, the at least the first will be easy to implement and will not bulk CCleaner.
1. In the tools section for Startup and Add/Remove programs, any new items in the list should be highlighted. This would attract the user's attention at a glance to anything new which maybe shouldn't be there. "New" can be taken to mean anything which has appeared in the last x days or anything which has appeared since the list was last viewed.
2. In the cleaner section add an option to overwrite free space on the drive. This is to help prevent anything which has already been deleted from being recovered. Just in case stuff in the sensitive past has been deleted without being shredded. Paranoid users will like this option.