Evidence Eliminator will save you the hassle of removing them manually. It's a real good program. I ran the entire Forensic Utility Suite on one of my boxes and recovered a shitload of data. I ran Evidence Eliminator with the wipe set at Zero + Reverse + Random (DOD) with 9 passes (the DOD spec is 7) and ran the Forensic again. It worked like a charm.
I'm not sure that it removed all the "really hidden data" mentioned on that site, but I know it handles the majority of the files/folders listed. After I ran it I could even see the hidden Content.IE5 folder inside the temporary internet files directory.
At the very least, people should run a disk wiping program like FreeWipe included with the PGP freeware, every so often. It's amazing how many people think they're safe after deleting their data. I used to think formatting would totally take care of it.