Just found this thread, but have been seeing this problem for a few months.
2008 iMac, Snow Leopard (clean install), minimal peripherals, short cables, no wireless anything. No weird 3rd-party software. No gaming.
The only atypical items I have are a new Wacom tablet, and a newly-installed Samsung internal SSD.
Never owned a WD drive of any kind; OWC ext HDDs are typically Hitachi. All HDDs are set up as single-partition.
Did the PRAM and SMC after problem was several weeks old, per OWC's direction.
Unmounting problem started after adding an OWC Qx2 4x2TB enclosure, configured as JBOD via FW800. Not only unmounting, but inability to perform other (seemingly unrelated) tasks, and goofy Sleep / Restart / Shut Down behaviors. Many error messages (mostly "-50"). Simply put, when the Qx2 was removed, and replaced with a single ext HDD (also OWC), no issues. I finally got an RMA replacement from OWC, and overall everything works MUCH better, BUT – the unmounting did resume, although only twice (yesterday and today) since last week's reinstall.
I don't believe files are corrupted, but can't really know that until I encounter one.
To me it doesn't seem like OSX, but I'm not remotely an expert. But after discussing this with the tech who installed the internal SSD, and the fact that a replacement enclosure works much better (the same 4 Hitachi drives have been retained throughout), I wonder if there is some finicky power supply and/or voltage spec that is causing intermittent failure to recognize. Something that could be fixed with firmware on Apple's part?
Just adding to the pile.
Thanks for this thread. Will take a look at some of the recent suggestions.