Well, a lot is determined by your host. If you have your own server I would suggest using a networking tool like JGN (sorry, but it just makes sense)
http://javagamenetworking.dev.java.net, but if your server will not allow you to deploy your own server application then you could write something as a JSP, JSF, PHP, Perl, ASP, etc. that you could simple create a URLConnection to the URL where your script and include elements in the GET or POST that you want to send to the server and it could generate the file(s) accordingly. The same for pulling the information back. If you decide to go this route you might find some more extensive wrappers for URL requests like the ones in the Apache Commons useful.
-Matt Hicks