I'm new to ccleaner. When I did the analyzer, then clicked "run cleaner," and it said it would permanently delete files. Does this delete everything that is on the right side including all of Microsoft applications, adobe, office 2007, Silverlight, etc...Kind of worried to run cleaner. I can't lose all of my applications.
It wont uninstall the applications. It will remove their left over files (logs, caches, etc).
If you don't want it to "super-clean" Microsoft Office 2007 you may want to untick that box, it will clean much more than the MRU (recent files list) in it.