Ok, I think we can solve both of those problems with the same thing. Try something like this:

#!/usr/bin/perl

$nf="endo";

foreach $file (@ARGV) {
   open (PASSWD, "$file") || die "Couldn't open $file\n";
   while (<PASSWD>) {
     ($login, $passwd, $uid, $gid, $gcos, $home, $shell) = split(/:/);
      $USERS{${file}.${login}} = $gcos;
           #this way the first key is "passwd.server1.root"
   }
   close (PASSWD);
}

open (NEWFILE, ">$nf");

foreach $login (sort keys %USERS) {
   print NEWFILE "$login, $USERS{$login}\n";
}

close (NEWFILE); # just because I'm tidy
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and now you call your script with script.pl passwd*