There are several ways of doing this(
EJB,
Servlet) but I would suggest using RMI for it's clarity of execution (less overhead that EJB, and, without custom fiddling, more secure that a servlet). You can have you applet make a connection to you RMI server implementation and then you have complete access to the IIS server as if you were executing the call from the server's environment. Look for RMI applet chat apps for a starting point of how to make the connection back to the server.
Sean