Something like the magic you want is in wrapLine at the end of the code. However take note of the other changes I've made to your sample code. In particular:

• Don't use global variables.
• Don't use prototype subs
• Don't call subs using &
• Use three parameter open and lexical file handles
• Declare variables in the smallest scope that makes sense

#!/usr/bin/perl

use warnings;
use strict;
use Time::Local;

my $kMaxLine = 70;

#Will hold the command line data from the execution of module "add_use
+rDefined" (my $module_cmd = "$0 @ARGV";)
#But for now hard-code in an example.

appendToFile(
    '/mrtg/mrtgwww/cfg/devices/Tests/Router-Memory_and_Storage.cfg',
    './add_userDefined --cfg=Router-Memory_and_Storage.cfg --host-temp
+late=In-Progress/Memory-and-Storage.htp --if-template=In-Progress/Mem
+ory.template --ip=10.10.10.10',
    );

sub appendToFile {
    my ($cfgFileName, $module_cmd) = @_;
    #Get ONLY the Month and the Year
    my ($sec, $min, $hour, $mday, $mon, $year, $wday, $yday, $isdst) =
        localtime();
    my %months = (
        0  => 'January',
        1  => 'Feburary',
        2  => 'March',
        3  => 'April',
        4  => 'May',
        5  => 'June',
        6  => 'July',
        7  => 'August',
        8  => 'September',
        9  => 'October',
        10 => 'November',
        11 => 'December'
        );
    $year = 1900 + $year;
    my $month_year = "$months{ $mon } $mday, $year";
    my $cfgmaker_cmd;
    my $wholeFile;

    #open my $dataIn, '<', $cfgFileName or die "Error opening $cfgFile
+Name: $!\n";
    while (my $line = <DATA>) {
        next if $line =~ /^# Created by/i;

        if ($line =~ /\/jwpmrtg\/bin\/cfgmaker/i) {
            chomp($line);
            $cfgmaker_cmd .= $line;
        } else {
            $wholeFile .= $line;
        }
    }

    #close $dataIn;
    $_ = wrapLine($_) for $module_cmd, $cfgmaker_cmd;

    my $sep = '#' x $kMaxLine;
    my $comment .= <<EOF;
$sep
##        Date: $month_year
##   Module CMD: $module_cmd
## cfgmaker CMD: $cfgmaker_cmd
EOF

    $comment .= "$sep\n";

    print $comment;
    #    print $wholeFile;
}


sub wrapLine {
    my ($line) = @_;
    
    $line = '' if ! defined $line;
    return join "\n##      ", $line =~ m~(.{1,$kMaxLine})(?:\s|(?<![-.
+\w=/]))~g;
}

__DATA__
[download]

Prints:

######################################################################
##        Date: Feburary 8, 2012
##   Module CMD: ./add_userDefined --cfg=Router-Memory_and_Storage.cfg
+ 
##      --host-template=In-Progress/Memory-and-Storage.htp 
##      --if-template=In-Progress/Memory.template 
## cfgmaker CMD: 
######################################################################
[download]

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