One of the issues that running maintenance tools like Disk Utility can run into is that as long as you're booted to the disk, it's difficult to run diagnostics against it or change files currently in use. IceClean runs many of those utilities at the command line behind a simple UI to get around some of those problems. The app will do the usual tasks, like verifying and repairing the system disk, disk permissions, and cleaning up orphaned .plist preference files, as well as help you kill a hung Dashboard or Dock, and much more.
IceClean can be configured to run on a regular basis, or only when you need it. The app is free, and requires Mac OS 10.5 or later.