Onyx is one my favorite apps in this respect, because it'll also run maintenance scripts on demand, and clean various system caches. CCleaner will also repair permissions on the startup disk (Disk Utility does that too, as do other applications such as Onyx, for example), and generally speaking, it's pretty harmless on an otherwise problem-free system. I can't in good conscience acquiesce to this: some applications are coded by very competent people (it's the case for CCleaner, whether for Mac or for Windows), and can actually do some good in the sense that they'll clean some files the average user won't even know exist, and free a little disk space in the process.
