WD, Seagate, and Toshiba drives
https://discussions.apple.com/thread/5518936?tstart=0
had this to say from Western Digital:
As a valued WD customer we want to make you aware of new reports of Western Digital and other external HDD products experiencing data loss when updating to Apple’s OS X Mavericks (10.9). WD is urgently investigating these reports and the possible connection to the WD Drive Manager, WD Raid Manager and WD SmartWare software applications. Until the issue is understood and the cause identified, WD strongly urges our customers to uninstall these software applications before updating to OS X Mavericks (10.9), or delay upgrading. If you have already upgraded to Mavericks, WD recommends that you remove these applications and restart your computer. If you have already upgraded to Mavericks and are experiencing difficulty in accessing your external hard drive, please do not save anything to the drive, disconnect the drive from your computer, and contact Western Digital Customer Service at http://support.wd.com/country/ for further assistance
Note, personally, Western Digital hard drives that are in Newertech Voyager removable drive stands are not impacted if they don't have Western Digital software.
Since Mac OS X 10.3, it has been possible that mismatched firmware and operating system updates could lead to hard drives becoming invisible that are hooked up while the update is being installed. It is strongly recommended that all users backup their data, dismount, and then remove any external drives before installing any update. If you don't know how to dismount, shut down the computer, and then disconnect it. Always check for software compatibility before installing a new operating system.
People making clones should be aware an erase may need to be needed, and reformatting with GUID partitioning to boot 10.7 or later:
https://discussions.apple.com/docs/DOC-3003
This has not worked with all Western Digital drives, and thus a firmware update would be needed for those drives where formatting does not make a difference.
Western Digital also admits under the specifications for its MyBook External drive 3 TB as sold on B & H Photo, that you need to do the following:
Mac OS X Leopard, Snow Leopard, Lion
Requires reformatting for Windows XP, Vista, 7
That means it probably under 10.7 and later is not able to handle the 64 bit nature of 10.7 and later, or the lack of Rosetta. For those upgrading from 10.6.8 and earlier, please read this tip:
https://discussions.apple.com/docs/DOC-6271
And it also has these pages on Mac compatible hard drives:
http://www.wdc.com/en/products/external/portableformac/
http://www.wdc.com/en/products/external/desktopformac/
Some Toshiba hard drives appear to have similar issues:
https://discussions.apple.com/thread/6079250
Seagate has some solutions for NTFS as well:
http://knowledge.seagate.com/articles/en_US/FAQ/216511en
This is a tip in progess.