Heh. MVS taught us all about batch processing systems and then Unix came along and taught us to forget everything that we had ever learned; that cron-jobs running every five minutes were the only way to go. Not true. Unix/Linux has plenty of good batch workload managers, all free. Use one. CPAN has all the tinker-toy parts, too. Use 'em. None of 'em require JCL and //JOB cards...
At this point we are using cron. But I have to agree that cron is not the only way and can stomp on you. If you are using a web server make sure you use authentication. You don't want just anyone to execute it. I have a Apache web server using Perl CGI with an admin page that is restricted, no sticky fingers if you please!