I used onyx for a while and system optimizer X, much the same. They are pretty useless and they give too many confusing options and alarming error messages. they only run internal scripts and clear caches.
If you are having problems then you are better off manually deleting a specific pref or cache file rather than clearing everything out. But as I said applejack is less confusing. Plus I guarantee you will enjoy watching it work in single user mode. You will feel much more geeky and powerful and it impresses the ladeez too.