When it comes to keeping your Mac's files and folders protected, you'd think Time Machine would have it covered. It's capable of backing up and restoring files and folders from any given time and – if you boot from your Mac OS X installation disc – can even restore your entire system.
That's fine and dandy, but if you hanker for a more traditional form of backup tool, then Carbon Copy Cloner has most bases covered. As the name implies, it can be used as a simple cloning tool – pick your OS drive as the source, choose your backup drive as the target and off you go: a perfect replica of your hard drive on your backup drive. This also enables you to upgrade a hard drive easily too: all you need is a spare drive bay or external enclosure, clone old to new, then install the new drive.
Carbon Copy Cloner also offers more features: it can be used to back up selected files and folders only, and perform incremental backups so only the changes to a drive are recorded on subsequent backup runs.
If the idea of giving over an entire drive or partition to a cloned backup of your main drive isn't practical, Carbon Copy Cloner can also back up to disk images too – choose New disk image... from the Target dropdown menu to create a dedicated file, which can happily sit on the backup drive without disrupting it (you can even store multiple images of the same drive at different stages in its life this way too).
The program is donationware – you're free to use it, but if you find it useful consider making a donation to the author and helping ensure its future development.