$hash{A}{B}{C}{D}{one} = "1";
$hash{A}{B}{C}{D}{two} = "2";
$hash{A}{B}{C}{D}{thr} = "3";

$hash{A}{B}{C}{E}{one} = "4";
$hash{A}{B}{C}{E}{two} = "5";
$hash{A}{B}{C}{E}{thr} = "6";

my @sort;
push @sort, [ $_, 'D' ] for keys %{$hash{A}{B}{C}{D}};
push @sort, [ $_, 'E' ] for keys %{$hash{A}{B}{C}{E}};
for my $ref ( sort { $a->[0] cmp $b->[0] } @sort ) {
    print "Key: $ref->[0]; Hash: $ref->[1]\n";
}
__DATA__
Key: one; Hash: D
Key: one; Hash: E
Key: thr; Hash: D
Key: thr; Hash: E
Key: two; Hash: D
Key: two; Hash: E