I have TuneUp installed in my system ... but never use it . Initially I have used it with windows 7, and got various troubles. Sometimes those troubles are hard enough to fix, and sometimes those are beyond any fix.
If you really want to use TuneUp, dont use it for more than these three functions
CCleaner, on the other hand , never gave me a chance to complain against it.
The Disk Cleanup utility inbuilt (found in Start > All Programs > Accessories > System tools > Disk Cleanup) can do it all the cleaning needed .
Finally, about registry hive , dont touch it at all, unless you are 100% sure what you are going to do .