Reg Cleaners can break poorly written programs.
I had a problem with MS Project.
It created a huge number of empty keys, which I purged with CCleaner.
The next time I tried to load my project (course assignment) MS Project claimed that the project file was corrupt.
I reinstalled MS Project and "lo and behold" my project file was no longer corrupt.
That's the only problem I've encountered though.
As jfuller05 said, create a backup when the option is offered to you.
