my @flat_data;

for my $file (keys %hoh){
  for my $letter (keys %{$hoh{$file}}){
    my $weight    = $hoh{$file}{$letter}{weight};
    my $intensity = $hoh{$file}{$letter}{intensity};
    push @flat_data, [ $weight, $intensity, $file ];
  }
}

printf "weight: %d intensity %d Filename: %s\n", @$_
   for sort {  $a->[0] <=> $b->[0]
            || $a->[1] <=> $b->[1]
            || $a->[2] cmp $b->[2] }
       @flat_data;