my @flat_data;

for my $file (keys %hoh){
  for (values %{$hoh{$file}}){
    push @flat_data, [ @{$_}{'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;