Program Files folder

You can use Tweakui to relocate many of the system folders. It can be downloaded from Microsoft from the following address.

http://www.microsoft.com/windowsxp/downloads/powertoys/xppowertoys.mspx

You probally know this allready but when you install a program you have the option to place the programs where you want.

one way is to slave that hd and install a new hard drive with windows c drive this way all your programfiles will now be on the slaved d drive.You can then simply create a shortcut to any non windows programs to your new c drive.
This is a good step as all your stuff will be safer on the slave should your current c windows drive become unstable or crash.

It is not recomended moving these folders as you have installed them and windows uses them from this location, if you do they will no longer work.
Otherwise you can simply copy them ( non windows) and then create a shortcut to them, if they are games etc.

If you want to make a backup of them thats is ok. Or use windows backup tool and backup the hard drive.