From the command line, $ perl -pi -e'tr/\015//d' *.{pl,pm,pod,txt} or whatever shell glob you want to pick the files. I think that one's in the FAQs.

Update: Ah, sorry, I misread, 

#!/usr/bin/perl
for (@ARGV) {
    open my $fh, '+>>', $_ or warn $! and next;
    seek $fh, 2, -1;
    if (<$fh> ne "\n") {
        seek $fh, 2, 0  # seek unneeded on many platforms
            and print $fh "\n";
        print $_, $/;
    }
}

[download]
(untested)

After Compline,
Zaxo

In reply to Re: Properly newline terminate a bunch of files on Unix by Zaxo
in thread Properly newline terminate a bunch of files on Unix by eyepopslikeamosquito

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