Option 1 — Go Piggybacking: If you've got an iMac or an Apple Cinema Display, one option is to get a Backpack from TwelveSouth. These little babies clamp onto the mounting arm of the display and act like a shelf, perfect for your hard drive. They even come with wire ties for cord management, and a silicone mat so that the spinning of the drive doesn't cause too much noise.
Option 2 — Hide Them in Plain Sight: I have three Western Digital My Book drives for various reasons, and until I can get a dedicated NAS unit, this is my best option. To keep them in the open to stay cool yet out of view, I hide them behind my Lego collection. Sure, it's a bit dorky, but you could put yours behind some books or a printer if you want, or get creative with your own ideas.
Option 3 — Velcro: For the drives that I want to keep portable yet want to keep off of my desk, I use industrial-strength Velcro to affix them to the bottom of my desk. Then I run the USB cable to a USB hub that's also secured to the underside of the desk, keeping things nice and neat. It's the best of both worlds, and the velcro is more than strong enough to hold up the drive. (Images: Kevin Whipps)