the quickest and easiest way to ensure that you are backing up everything that you need is to use the "ditto" command. Get yourself a cheap firewire drive and you can run this command in the terminal, and just like macgenious said, you will get that other 10% of invisible files and folders. It also retains all your permissions, ownerships, and groups on your files and folders. On top of that, it also copies the resourses in the files so that your Mac knows what to do with a file when you try to open it.
This is all done from the terminal:
sudo ditto -rsrc /Users/username /Volumes/firewiredrive/username
After that you can tar the folder or zip or gzip it. Whichever you prefer to compress and archive your files to. This is the basic way in which many admins backup thier systems. They issue commands (usually tar combined with gzip) and back the system up to another hard drive or tape device.
With retrospect, I agree that it's a good system, however it has some major limits in my opinion as having to do with permissions and ownerships when you have to unarchive stored data in Mac OS X. Hopefully it will get more productive as they keep developing for it...
Anywho, just another method of backing up your stuff.