I'm not sure what registry issues you could come into contact with, unless you installed an application to one of the other drives, which I'd not recommend. It should be easy to update individual programs to save/open from a new location.

When I read your original post, I thought you were trying to do something different. I thought you wanted to make three physically separate disks look like one drive. I'm not even sure that's possible... maybe with symbolic links...

But if all you want to do is take three drives of data and turn them into one, it should be a simple matter of copy and paste. If one of them is your system drive, though, you'll need a clone tool to help you migrate to the new drive. I didn't see in your post whether this was the case.

I agree with Christian that partitioning doesn't make much sense. You're better off just making three folders to represent the three drives.

For most programs, when you open them up and they don't see the drive/folder they're used to saving to, they'll simply default to another folder, usually the default Windows user folders like Documents. From there you can choose whatever folder you want.