my %hash = (
      APP1 => {
         error => {
            6001 => 10,
            6002 => 15,
            6003 => 25,
            },
         alert => {
            1001 => 2,
            1005 => 200,
            },
         warning => {
            0022 => 10,
            },
         },
      APP2 => {
         error => {
            6001 => 4,
            6004 => 21,
            },
         alert => {
            1002 => 3,
            1005 => 165,
            },
         },
      );

my %revhash;

for my $key1 (keys %hash) {
   for my $key2 (keys %{$hash{$key1}}) {
      push @{$revhash{$hash{$key1}{$key2}{$_}}}, $key1.":".$key2.":".$_
         for keys %{$hash{$key1}{$key2}};
   }
}

my $cnt;
for my $key (sort { $b <=> $a } keys %revhash) {
   for (@{$revhash{$key}}) {
      printf "%3d %3d %s\n", $cnt, $key, $_ if ++$cnt <= 5;
   }
}