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.