This is one possibility that may have happened to you. It did to me two weeks ago. Have you used Disk Utility to wipe the unused drive space?
I used the install DVD's version of Disk Utility to wipe my OS X partition's unused space. Unfortunately, the computer decided to have a case of the vapours, and it fainted dead away in a kernal panic.
To wipe unused space, Disk Utility creates a temporary file and writes zeros over every uncatalogued particle of drive space. This single, temporary file grows to enormous proportions but is removed at the end of the wipe. Because of the kernal panic, however, the huge file remained.
When I restarted the computer, a popup warned me that there were only eight megabytes of space remaining on the "drive" — in this case, one of four partitions that contains nothing but OS X. I place all my documents on another partition, and I knew I had 30 gigabytes of free space, at least.
I knew of the gigantic file but didn't know its name, so searching the web for more information, I discovered and downloaded Disk Inventory X so I could find it. But for some reason it did not reveal the file — or I screwed up and didn't know what to look for, though it lists file sizes. Maybe it can't inspect the system-core files. I don't recall whether it lists invisible files.
Further searching on the web revealed the space hog to be a "sparse" file, so using the free search utility EasyFind that I set to look for invisible files, it showed a file with "sparse" in its name, and the pathway to it.
Using the donation-ware app Invisibles, I set all files to visible so the sparse file would be easy to trash. But the system wouldn't allow me to do so. However, I have a G4 with System 9 on another partition, and as an OS X repair utility, OS 9 can't be beat.
I booted into 9, clicked on the 29-gigabyte-and-change sparse file and trashed it, rebooted into X, set the invisibles back to visible again, and everything was back to normal. (OS 9 also uses a dot in front of a file name to make it invisible.)
The easy availability of System 9 is a cheat — I haven't bothered to learn how to trash "untrashable" files using Terminal or any utility written for the purpose. But that wouldn't be hard.
Download EasyFind and Invisibles from versiontracker.com or macupdate.com. If you find a gigantic and invisible "sparse" file, that's your problem.