I've been using Cocktail for a while (when it was free) and like it just fine. Neither of theses utilities do anything you couldn't do with the tools Apple provides in OSX, but if it encourages users to do regular maintenance hassle-free, I'm all for it.
When OSX first came out, I created a sticky note with the UNIX commands and some notes; it's fairly easy to read the note while the terminal is open and run the scripts. Just like learning HTML and writing web pages with a text editor, this is a great way to learn proper UNIX syntax if you want to go further with it. You could even download the developer tools from Apple and write your own app that does the same things, if you wanted to learn a bit about application development on OSX. Otherwise, use a utility like Cocktail and forget about it.
I''m from the "if it ain't broke, don't fix it" school, but at least OSX makes it easy to run two similar programs and see what you like best, and trash the one you reject.
With OS9 too many bits and pieces got installed with each new app (with Windows, you have the added grief of registry changes, which is another way of saying the OS itself is altered), and it wasn't a good idea to play around like that; sooner or later a program you thought was gone would come back to haunt you.
So, I might give OnyX a try before I shell out $10 for Coctail (the old, free version still works just fine with OSX 10.2.6).