Most decent Windows editors have an option to enforce a particular line ending. Both ActiveState and PXPerl on Windows will respect either windows- or UNIX-style endings. Therefore, I suggest finding out how to set your editor to always save using UNIX line endings.
The Eightfold Path: 'use warnings;', 'use strict;', 'use diagnostics;', perltidy, CGI or CGI::Simple, try the CPAN first, big modules and small scripts, test first.