Number crunching is something that Perl is not very great at right now. I recently prototyped an algorithm in Perl. Once I was happy with it, I rewrote the core as an XS module. I got a 60-fold speed increase.

I like python's trick for making making a module a script. I.e. if you execute a file, it runs a main routine, but if you include it, it just imports functions, etc.