Why does the application in focus hang for several seconds when a drive spins up? This has happened to me for as long as I have used Macs, I think.

Occasionally, Mac OS X remembers a long-forgotten disk, sometimes external, sometimes internal, and spins it up for some reason. And every time this happens, the front-most application, the one I am using at that moment, hangs until the disk has spun up.

Why does that happen and can I tell OS X that the application in focus ought to have priority over hard disks? (Note that it is not the boot hard disk with the swap file that is being spun up.)
I know exactly what you mean
Mine does it with my external HD

It drives me nuts.
I've replaced my HD in my MBP with a SSD.
I've been thinking about replacing the SuperDrive with a hard drive tray and putting the original drive in it, but if my computer is going to hang to spin up the HHD it isn't worth it.

I guess I just have to buy one, install it, and see what happens.
I'll let you know Tuesday when the caddy tray arrives if it is an OS-HD issue, or a OS-USB issue