It's not a perl-specific answer, but when I've run similar jobs, I've used CGIwrap so that I can set limits on a per-user basis. (and then just run the jobs as a specific user)

See the option:

--with-rlimit-nproc=COUNT
limit number of processes with setrlimit

In this specific case, it won't queue things up, but'll reject requests if too many come in at once. (depending on your users, this might not be acceptable). I like it because I can get it to kill processes that run too long, and keep 'em from sucking down all of the server's memory.

What you really need to do here is to ... get to know networking and queueing. :-)

In other words, your website would be used to create and submit jobs to a batch-processing system on the same or on a different server, and to monitor the status of the jobs as they are completed. There are many batch and cluster management systems out there, and your website would serve as an interface to one.

Furthermore, you will discover that nearly all of these batch management systems already have a web-interface, so the entire need for your existing website may prove to be ... nonexistent.

unless you're just trying to learn :)