The registry cleaner in CCleaner is usually pretty safe to use. Registry cleaners are designed to remove fragments, invalid entries, blank spaces or gaps, etc... from the registry to help keep it nice and orderly to improve it's read speed at startup.
However, some registry cleaning programs (not CCleaner) are a little to aggressive in what they find and can cause problems in Vista if the wrong item is allowed to be deleted from the registry.
It is best to always have the program create a backup of what it is removing from the registry to restore later if needed.
Hope this helps,