When your harddisk starts to make odd noises, it is often too late: your data becomes corrupt and Windows usually fails to properly read from the partition. So what to do? Get a new HD and try to rescue what you can. A great tool to assist you in doing so that I came across and used successfully is File Scavenger from QueTek.
This small tool will scan your partition (even if Windows can’t read from it anymore) for files and will restore everything it can. It’s always bad when you need such a tool, but it’s good to have one then.
If your HD supports SMART, you should always use a SMART monitoring tool; this way, you’ll know early if your disk has any problems.