Under linux (certainly Debian, I assume the rest do it as well), the command sdparm will spin down hard drives. Hdparm will do it for pata drives, sdparm for sata and external usb ones. Specifically
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sdparm -C stop /dev/sdX
There's a few ways to implement this. I just tagged a an instance of this command for each drive onto /etc/rc.local, meaning every time I rebooted I heard them all spin up then proceed to spin down again shortly afterwards. This suited me, but clearly once spun up (a second time) they stayed up.
A clever way around this can be found here, I personally just spun them down manually when I was finished working with them.
Past tense as the entire damned lot have failed (Samsung F1s, if curious) and I've not bothered to rma them yet.