I think you might have a couple problems in the "doReplace" sub, because of how you build the replacement regex:

   my $regex = "s/$old/$new/g";
[download]

• If you put "\Q" and "\E" around "$old" in that regex, the periods in the IP addresses and host names will only match literal periods; as it is, they will match any character (e.g. "123.1.3" also matches 123.1[012]3)
• You also need to anchor that regex -- as it is, if $old is "box.my.dom", it matches "thisbox.my.dom" and "thatbox.my.dom"; the same applies to IP addresses, especially when doing your router files, where you change only the first three components -- if $opt_oldip is "123.123.123.4", your regex looks for any occurrence of "123.123.123", which would include "89.123.123.123"

On top of that, you're taking it for granted that the command line option strings really are valid IP addresses and host names, and you're putting them into a shell command that you then pass to a single-arg system() call. Personally, I'd feel better if these were checked first -- better still if you don't put the one-liner perl script on the command line at all.

In terms of simplifying things (while also fixing the problems above), you could consider something like this (untested):

#!/usr/bin/perl

use strict;
use Getopt::Long;

# ... define arrays of file names, then ...

my ( $opt_ip, $opt_host );
GetOptions( 'ip=s' => \$opt_ip, 'host=s' => \$opt_host );

my $Usage = "Usage:  $0 [-ip old:new] [-host old:new]\n";
die $Usage unless ( $opt_ip =~ /\S:\S/ or $opt_host =~ /\S:\S/ );

my $ipreg = qr/\d{1,3}(?:\.\d{1,3}){3}/;
my $hostreg = qr/\w+(?:\.\w+){2,}/;

if ( $opt_ip ) {
    $opt_ip =~ /($ipreg):($ipreg)/ or die "Bad value for -ip: $opt_ip\
+n $Usage";
    my ( $old, $new ) = ( $1, $2 );
    doReplace( $old, $new, 'IP', \@ipFiles );

    s/.\d+$// for ( $old, $new );
    doReplace( $old, $new, 'RTR', \@routerfiles ) if ( $old ne $new );
}
if ( $opt_host ) {
    $opt_host =~ /($hostreg):($hostreg)/ or die "Bad value for -host: 
+$opt_host\n $Usage";
    my ( $old, $new ) = ( $1, $2 );
    doReplace( $old, $new, 'HOST', \@hostFiles );
}

sub doReplace
{
    my ( $old, $new, $typ, $files ) = @_;
    open TMP,">/tmp/$typ-config-editor.$$.perl" or die "can't write sc
+ript file: $!"
    print TMP "s{\\b\\Q$old\\E\\b}{$new}\n";
    close TMP;

    for my $f ( @$files ) {
        my $cmd = "perl -i .bak.$$ -p /tmp/$typ-config-editor.$$.perl 
+$f";
        print "cmd: $cmd\n";
        # system( $cmd ) or print "\t $f changed\n";
        # (system returns exit status of $cmd: 0 for success)
    }
}
[download]

That still has the potential for trouble when editing the router files, if they contain any full IP addresses where the latter three components might match the first three components of the "old" IP address. If that's really a risk, you'll need to write a special one-liner script just for them.

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