I must admit that I don't have too much to add to the informative answers already supplied, but I do have some experience with Apache CGI that leans a bit toward AS.

I develop under the Apache for Win32, which does not/cannot be told about the Cygwin environment. CGI scripts that are written for this server have an easier time if written in AS, there's less mucking about with filenames and paths than the cygwin distro.

Offsetting that is the ease of implementing modules under cygwin/CPAN. Sometimes I'd like to create a snazzy CGI app that uses some module that may not be compiled as a PPM yet (Image::Magick comes to mind, but it's a PPM now). Under those circumstances I usually punt and wait till I'm near one of my linux boxes.

Anyone here played with cygwin cgi scripts under Win32 Apache?

Overall, I believe your problem is a good one - Which of two fine perl implementations to use!

Good Luck