If you run your script on Windows, the carrage return and newline will both be removed (since it's expected that under Windows files will end in both a carriage return and a newline).

That's completely wrong. Perl automatically converts CRLF to LF when reading text, so $/ is set to LF ("\n"). Your script shouldn't see CR at all, so chomp only removes the LF.

Now, if you were dealing with binary data, chomp won't work (without changing $/) because chomp is a text function.

print(unpack('H*', $/), "\n");    # 0a          Just LF

my $str = <DATA>;
print(unpack('H*', $str), "\n");  # 746573740a  No CR

chomp($str);
print(unpack('H*', $str), "\n");  # 74657374    LF chomped.

__DATA__
test
[download]

If, on the other hand, you want to run a script that will strip the EOL marker off a file regardless of what OS the script is running on and whether that file came from Unix or Windows, you need to do that yourself, with something like:

That regexp is incomplete. It doesn't handle systems that use \r as the EOL marker.