How about some <> magic:

#! /usr/bin/perl
#Call the scripts with <scriptname> passwd.*

while (<>) {
       ($login, $passwd, $uid, $gid,
        $gcos, $home, $shell) = split(/:/);
       $USERS{$login} = $gcos;
}

$nf="endo";
open (NEWFILE, ">$nf");
foreach $login (sort keys %USERS) {
       $gcos = $USERS{$login};
       print NEWFILE "$login, $gcos\n";
   }
[download]

Now just call the script with the passwd files as arguments(or even with passwd.*). The <> in the while will automatically open each file in turn and read it in for you. I also moved the opening of NEWFILE to the end of the script since that's when you actually have to have it open.

Later