How do I put a cut/copy reference to specific files and/or folders into the Windows clipboard so that when I open standard Windows Explorer window, go to somewhere
If you're using Windows Forms, look at System.Windows.Forms.Clipboard. I think that should be able to do that. I'm not sure how to do what you want since I've never looked in to it, but I'd look at the FileDropList methods (GetFileDropList, etc.) first since they look promising.
If you need to find out if it was a copy or a cut and similar more detailed information, it seems like you'll have to use the IDataObject interface.