OK, here is my version (which also handles IPv6). It does the famous nm5.in in just under 3 seconds (your original code takes about 3.5 seconds and you new more-than-4-octets code takes over a minute -- no, I don't know why so slow for me), on one computer. It also appears to handle ranges that include 255.255.255.255 which it doesn't appear either of your versions do properly (see nm3.in).

The major differences are that I "clean as I go" and I use single bitwise operations on strings when possible. This is so much faster and smaller than Net::CIDR, that I'm tempted to make a drop-in replacement for that module based on this (though I'll probably get side-tracked before that happens).

package CIDR_Lite;

use strict;

use vars qw($VERSION);

$VERSION= '0.03';

my $cache;

sub _setCache {
    my $nBytes= shift;
    my $nBits= 8*$nBytes;
    my $h= $cache->[$nBytes];
    if(  ! $h  ) {
        $h= {};
        $h->{zero}= my $zero= "\0" x $nBytes;
        @{ $h->{mask} }= (
            map {
                pack( "B*", "0" x $_ . "1" x ($nBits-$_) )
            } 0..$nBits,
        );
        @{ $h->{width} }= (
            $zero,
            map {
                pack( "B*", "0" x ($_-1) . "1" . "0" x ($nBits-$_-2) )
            } 1..$nBits,
        );
        $cache->[$nBytes]= $h;
    }
    return $h;
}

sub new {
    my $proto = shift;
    my $class = ref($proto) || $proto;
    my $nBytes= shift || 4;
    my $self= {};
    @{$self}{qw( mask width zero )}=
        @{_setCache($nBytes)}{qw( mask width zero )};
    $self->{nBytes}= $nBytes;
    $self->{nBits}= 8*$nBytes;
    bless $self, $class;
}

sub _plus {
    my $self= shift;
    my $base= shift;
    my $bits= shift;
    my $res= $base | $self->{width}[$bits];
    while(  $res le $base  ) {
        $res &= ~$self->{width}[$bits--];
        return "\xff"x(1+length($base))   if  $bits < 0;
        $res |= $self->{width}[$bits];
    }
    return $res;
}

sub add {
    my $self= shift;
    my $input = shift;
    my( $ip, $bits )= split "/", $input;
    my $start= pack( "C*", split /\./, $ip ) & ~$self->{mask}[$bits];
    my $end= $self->_plus( $start, $bits );
    ++($self->{ranges}{$start})
          ||  delete $self->{ranges}{$start};
    --($self->{ranges}{$end})
          ||  delete $self->{ranges}{$end};
}

sub clean {
    my $self = shift;
    my $ranges= $self->{ranges};
    my $total= 0;
    for my $key (  sort keys %$ranges  ) {
        if(  0 == $total  ) {
            die "Impossible"
                if  $ranges->{$key} <= 0;
            $total += $ranges->{$key};
            $ranges->{$key}= 1;
        } elsif(  0 == ( $total += $ranges->{$key} )  ) {
            die "Impossible"
                if  0 <= $ranges->{$key};
            $ranges->{$key}= -1;
        } else {
            delete $ranges->{$key};
        }
    }
}

sub list {
    my $self= shift;
    my( $start, $total );
    my @results;
    my $zero= $self->{zero};
    for my $ip (  sort keys %{ $self->{ranges} }  ) {
        $start= $ip   unless  $total;
        $total += $self->{ranges}{$ip};
        if(  0 == $total  ) {
            my $end= $ip;
            my $bits= $self->{nBits};
            while( 1 ) {
                $bits--   while  $zero eq ( $start & $self->{mask}[$bi
+ts] );
                my $next= $self->_plus( $start, ++$bits );
            last   if  $end lt $next;
                push @results,
                    join(".",unpack"C*",$start)."/".$bits;
                $start= $next;
            }
            my @temp;
            $bits= $self->{nBits};
            while( 1 ) {
                $bits--   while  $zero eq ( $end & $self->{mask}[$bits
+] );
                my $next= ~ $self->_plus( ~$end, ++$bits );
            last   if  $next lt $start;
                push @temp,
                    join(".",unpack"C*",$next)."/".$bits;
                $end= $next;
            }
            push @results, reverse @temp;
        }
    }
    wantarray ? @results : \@results;
}

1;
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Updated: Thanks to runrig for catching a couple of hard-coded 32s that got left in.

        - tye (but my friends call me "Tye")