Here's a more generic way to flatten a hash with an arbitrary number of levels. It can be easily extended to handle embedded array refs, as well:

#!/usr/bin/perl -w
use strict;

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 $separator = '.';

sub flattenHash
{
    my $hashRef        = shift;
    my $prefixArrayRef = shift || [];
    my $outputArrayRef = shift || [];
    while ( my ( $key, $value ) = each(%$hashRef) )
    {
        push @$prefixArrayRef, $key;

        if ( UNIVERSAL::isa( $value, 'HASH' ) )
        {
            flattenHash( $value, $prefixArrayRef, $outputArrayRef );
        }
        else
        {
            push ( @$outputArrayRef, join ( $separator, @$prefixArrayR
+ef ),
              $value );
        }
        pop @$prefixArrayRef;
    }
    return wantarray ? @$outputArrayRef : $outputArrayRef;
}

my %flatHash = flattenHash( \%hash );

my @sorted =
  sort { $b->[0] <=> $a->[0] } map { [ $flatHash{$_}, $_ ] } keys(%fla
+tHash);

foreach my $arrayRef (@sorted)
{
    print "$arrayRef->[0] $arrayRef->[1]\n";
}
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update: made sure of no value collisions in reverse, quoted octal key.