External hard drive freezes main thread in OS X Lion
This is somehow one of the most frustrating things around for me as well.

I want to allow my mac to spin down the hard drives when they are idle, but this makes for long delays (on the order of 3-5 seconds normally and on occasion even longer).

Quite simply, allowing those connected devices to block the fseventsd and other system level daemons means putting up with long delays when you don't really want them.

You can and should turn off the sleeping drive to prevent intermittent slowness.