There are quite a few binary distributions of Perl for Win32 available besides the two you mention. The primary advantage of cygwin Perl is that you get a working fork (not a badly emulated, slow, buggy, imitation fork). The primary disadvantage is that you need to install cygwin, which probably means the install is approximately an order of magnitude less simple.

For replacing *.bat files, you don't need to a real fork. So I'd go with a smaller distribution than cygwin in your case (though I do recommend installing cygwin in the general case -- though I don't use cygwin Perl much personally for no particular reason, though, I suspect it prefers cygwin path treatment which would be a pain at times). I'd probably not go with ActiveState, personally, if for no other reason than I like to support competition and having a near monopoly even for Win32 Perl distributions is something I prefer not to contribute to. (:

http://www.cpan.org/ports/#win32 gives a good list but it isn't always complete, unfortunately, but it gives you some other choices in case you are interested.