CCleaner is a fairly powerful tool and it can be misused, but it generally won't delete anything of importance. It's always a good idea to review whatever you're deleting. But I've never experienced any problems with it. You should be in good hands with this program.
truenorth,
I can't say what disabled your Limewire, nor can I say that it wasn't CCleaner. However, CCleaner only deals with specific folders and files, so maybe Limewire was somehow installed in a temp folder. I really don't know. I don't use Limewire anymore, but it's on my computer (4.12) and it works just fine and I do numerous CCleaner scans each week.