The way i prefer to keep my scripts constant across windows and linux platforms is to do two things...

1) always create/edit/save files in the UNIX format. (most decent text editors will have this as an option).

2) find out the path of the perl binary for linux and then (for windows) copy the perl.exe binary to the same path...

for example:
on my linux box, i've got perl under '/usr/bin/', so on my windows machine, i created the directory 'C:\usr\bin\' and copied my perl.exe binary into that directory (make sure you've got all your perl directories (lib, inc, bin, etc...) in the windows PATH, or else it'll grumble and complain)
(Or, you could just install the perl distribution directly into the directory 'C:\usr'...)

along with the windows port of apache i use, and activestate perl distribution, my scripts are identical across linux/windows platforms...