ok, on the CLSID thing, it's a location for COM registration. It's houses the inforamtion for shared DLL and files. Don't delete anythign from there. You risk the chance of screwing up something. The information is loaded so that you don't delete a file by acident that is needed by another application. It's called reference counting and is very important in MSI based installers. They will remove the reference when the application is removed, but as long as the value existed before hand it won't delete it.
You best bet is to simply leave the registry stuff behind.
I find it funny that people thing it will help speed up their machine by removing a few little entries in the registry. It's really not going to help you unless you have a corrupt hive.
anyway, values in HKLM\software\classes and HKCR shouldn't be messed with unless you know what you are doing. trust me on this, it's part of what I do for my job, so I know a little about it.