How does one develop a Perl/CGI application for a remote Unix-based server when your home box is just some flavor of Windows?

Find a throwaway box to install Linux on. Seriously. Someone near you probably has a P-II or P-III box that's way underpowered for Windows, but which will run Linux (or FreeBSD) just fine. A 133Mhz Pentium with 128Mb of RAM running headless (i.e., no X) Linux with Apache and MySQL isn't going to break any speed records, but it's good enough to develop on. You don't even need a monitor; set the box up to look like your ISP, and use putty for an ssh session into it. Or invest $45 for a 2-port KVM.