You can set up a web site on your desktop. Set an Static IP for it. Copy files (that you want to copy to your kindle) to a folder.
On your kindle, browsing your own website and download those files.
Currently, I'm using IIS to do it (it's free).
It seems like you're not asking how to do it but you want to do a market research before you write somekind of program to do it. lol.