For any modules installed into the @INC directories (including all standard modules), there should be no migration problem whatsoever. For any modules you've put in other places, there's really nothing for it but to find all the use lib statements and convert 'em. Fortunately for you, there's this programming language that's pretty good at that sort of thing ... =)

One way: First decide where you're going to put your libraries on the Unix-type system. Use a hash as a translation table, where the keys are windows directories and the values are your *nix correlates of those directories. That should make writing a script that updates all your perl scripts.