i'm not sure i agree that you are sorting by domain. domains are grouped, but the overall order of the result is strange. however, i think the following sub does what most people would expect:

sub sort_domains
{
    map { ${$_->[0]} }
    sort {
        my ($pa, $pb, $rv) = ($#{$a->[1]}, $#{$b->[1]}, 0);

        do { $rv ||= $a->[1][$pa] cmp $b->[1][$pb] }
            while (!$rv and $pa-- and $pb--);

        $rv ||= ($pb >= 0) ? -1 : ($pa >= 0) ? 1 : 0;
    }
    map { [ \$_, [ split /\./, $_ ] ]  } @_
}
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you can use it like so: my $noodle = join $/, map { sprintf "%64s", $_ } sort_domains keys %hosts;

p.s. let the golf begin

p.p.s. why $noodle?

update: fixed logic bug in line that deals with extra domain parts ($rv ||= ($pb >= 0) ? -1…)