One of the best tools I have found for developing Perl code within a Windows environment for use on a Linux server is the editor jEdit.

This editor has the ability to select the type of line break to use, provides good syntax highlighting, and all the other basics. The thing that sets it apart though are the plugins available.

The plugin I have personally found to be the most useful is the FTP plugin, allowing you to work directly against a Linux box from your Windows machine, even over an sftp connection. There are a number of others that make life as a programmer much easier as well, just look through and choose for yourself.

Of course, as was pointed to in a post by marto, make sure to read through the Setting up Perl/CGI with Windows guide written by Ovid. This will help you get past a large number of the basic snags to running your code on a Windows box.