If you have any experience with Linux, boot up a machine with a LiveCD then connect up the external disks. Chances are good that you will be able to at least look at the contents to figure out if it's the one you want to mark. This also gives some level of protection against infections on the drive, especially if they came from Windows machines.
Of course, in the future as soon as you pull a drive out of a machine you're going to write on it with black sharpie, aren't you?
I typically do this when I put a drive in or make any changes to a machine. The inside of a desktop case is great for writing things like "21 May 2015 replaced power supply". It gives you a history as soon as you open the case, even if hardware has failed.
Just my opinions, feel free to disagree or ignore.
I usually use small stickers that I put on the connector side of the hard drives. The Linux machine idea is pretty neat, but I don't want to take any chances, like ever. If something's infected, it has to go.
That's why Linux LiveCD or equivalent (WRT taking chances). Boot from a CD-ROM, rest of filesystem live in RAM, so the worst that happens is hit the big red switch and kill power. To be overly cautious, you could even unplug other harddrives. It sounded to me that your goal was to be able to identify the one drive out of a bunch that you wanted to save; I based my suggestion on that. Drives that you don't want could even be wiped from the LiveCD environment: use dd with /dev/null as the input, start at block 0 of the raw disk device, use fdisk/gpartd to overwrite partition tables. A bit of consulation with Professor Google should lead to other utilities that would securely wipe a drive.