This really depends on what you are doing. The ^M delimiter should only show up in other utilities, and even if you get them in Perl they are fairly straight forward to strip.

basically you really want to make sure that all of the modules you want to use are able to work on both OS's, I have found that many of the things (even most) work as good in Windows as in Unix.

The other thing I would recomend, get the OS type right off the bat in all your scripts, this gives you the ability to split off into different paths later in the script if you need to use system or exec. However since you did not give a clue as to what your scripts are doing this may or may not be relevant.

"Nothing is sure but death and taxes" I say combine the two and its death to all taxes!