OnyX is a very safe utility, and free. If nothing else, use it to empty the trash and keep it around in case it's needed again. I have had it for years and it has never caused any problem for me.
What Jon says is true as long as you use the version that is specifically for the version of OS X you are running. Neither earlier or later versions are safe to use. Of course that is equally true of virtually all utilities that perform system functions.
