OS X has a built in function to run so called cron scripts that fix your file system and hard disk in general. It's scheduled to run automatically during the night if the computer is idle. Some essential operations run every night, others only once every week or every month. So if you want your Mac to be healthy the most important thing you can do is to leave it running overnight, especially if you have worked on it all day and moved around big files.

If you have an iBook or Powerbook, you might want to keep it running once in a while or use Cocktail that allows you to run the same scripts at any time of the day.