I have this problem as well, with a 500GB Western Digital USB 2.0 MyBook. It's very annoying, especially when you're not even saving or opening anything, like just when I'm browsing the web, I want to type into the search bar, and the whole system just freezes for 5 seconds while the drive spins up, and then I can type again. There is absolutely NO need for that, the drive only contains movies, it's ridiculous!
I'm no computer engineer, but I know for sure that searching the web doesn't require an external drive containing movies to spin up, and even if it must spin up, it doesn't require my entire system to freeze during that period of time. It's like when on Windows you eject a CD, the system freezes for a few seconds while the CD tray is being ejected, it's retarded! But that actually makes some sense since you DID ask the CD to be ejected... But it still shouldn't freeze...
Bad programming!