First of all, did you check to make sure that there is no disk in your optical drive that might bork your boot?
Secondly, before you unplug or plug any internal drives (or any cable on the motherboard), make sure that the computer is completely shut down and that the computer is unplugged from the wall. This precaution is not to protect you -- it is to protect you from bricking your motherboard.
By the way, you only need to disconnect the power plug to disable a drive. Don't bother with the zillion-pin signal cable.
Thirdly, get/burn a live CD and keep it handy.
Parted Magic is a great live CD. It's small, it's easy to use, it's got a lot of tools and it only asks one question at boot. Such a live CD can do wonders when assessing computer problems (regardless of whether or not you run Windows, Mac or Linux/BSD.
For instance, someone in this thread suggested that you unplug all hard drives except your boot drive to see if you still hear the noise. Well, with a live CD, you can unplug
all of your hard drives and still run your computer! In that scenario, if you hear the noise, it is either your optical drive or one of your fans (or you need to feed the gerbal on the treadmill inside your machine!).
In addition, Parted Magic has some antivirus and disk health tools, which would be less destructive than trying to run recovery off of one of your hard drives, if it is it truly is in trouble.