Mac hard drive almost full; diagnostic apps do not explain why
Is this a MacBook? I ran into something similar and it turned out to be the local Time Machine snapshots. This was a new feature in OS X 10.7 Lion. Some programs show that space as used and some don't. Finder doesn't show that space as used but Disk Utility does.

Make sure to run WhatSize in "As Admin" mode to get an accurate representation of your disk usage. This isn't available in the App Store version. In that mode it will show you the local Time Machine snapshots.

Here is more information about local snapshots.