May I ask why you mentioned Tomcat and IIS?
If all you want to do is run a Java program from start to finish, then wait a while, then run it again (and so on), using a batch file invoked by the OS scheduler seems a reasonable approach. If you build your program as an executable jar file you could probably get away without the batch file, if that helps to make it simpler.
Or do you mean that you want to run some code which is already available as a
servlet or
JSP (or whatever), and need to request a certain URL from time to time?
Please explain a little more for us. Thanks.