External disk stalls iMac
What is going on is that OS X (actually it’s the Finder and the I/O subsystem) is “waiting” for the drive to be readable. 

Truth is, is not the “whole mac” but the Finder (and any Finder application) what freezes. For example, a Save/Open dialog, Time Machine starting, a Finder window, etc. However you can always cmd-tab and perform other actions.

There isn’t much you can do, except to tell OS X not to sleep your hard drives (or wait for the drive to spin up):

. Beware with that option, because it will mean that your hard drives are on all the time, thus degrading their lifespan. 

I’m not 100% sure if that option affects Firewire/USB external drives, but I think it does.