Originally Posted by Sharakkhal
If most of your data is in the My Documents folder, simply tell Windows that you'd rather My Documents were on the D drive. That way, if you have to do a recovery of your System Drive (C, it won't harm your data on the D drive (you'd just need to tell it to move stuff again after a recovery, but don't let it move the default My Documents data to overwrite your data in the future.
To do that, right-click My Documents, click Properties. There, you'll have a Target tab. Change that to be D:\My Documents and click Apply. It should ask you if you want to move your data to the new location, so just answer Yes and it will move the stuff over for you.
You'll still be able to access the stuff through the same My Documents shortcuts, it will just actually reside in a different location.