Permissions sometimes is not repaired properly by these utilities, unless you use Disk Utility of the boot drive. The real danger of prebinding utilities is you can render your Mac unbootable: The real danger with many of the other utilities which specifically empty system caches is that caches can get corrupt, sometimes requiring a complete erase and install to resolve a persistently corrupting cache file. Moral of the story, backup first, worry about alternate utilities later. If you don't have a backup, some troubleshooting utilities can actually dig you a deeper hole, whereby data recovery is the only way to restore your situation with expensive data recovery companies. Everything else should be treated as an after backup utility used only, and I repeat only for troubleshooting, when you know what it is you are troubleshooting, and are ready to restore the backup if the troubleshooting doesn't save you time.

The only safe utility to use is a backup utility. It is not a maintenance utility despite others calling it, Cocktail, Macaroni, Applejack, Jaguar-Tiger Cache Cleaners, and other multifunction utilities that do more than one task. Actually I wouldn't go as far as to say Onyx is safe to use.