I've used .Mac's Backup and I've used Retrospect. Simpler than either of those is simply dragging and dropping. Just copy the folders you want to backup onto your external drive. The only hitch I've had with this is that Quicken saves its data files in a strange place rather than putting them in the user's home folder--so I have to take 1 more step to do that.
Main benefits of not using a special backup application are the cost (free) and you don't need an application to use your backup. You can pull individual files out if you want. It's more flexible.
The main disadvantage to not using a backup app is the lack of scheduling your backups--it's all manual. But you might be able to schedule them with an AppleScript. If you do want automatic backups, then do as DavidLeblond suggested and use the command line.