For interest. May not be suitable in production code. ;)

use strict;
use warnings;

my %hash;
my $counter;

while (<DATA>) {
    chomp;
    my ($key1, $key2) = split;
    $hash{$key1}{$key2}[0] = ++$counter;
}

printf "%-12s%-12s%-12s\n", @{$_}[1, 2, 0] for ['Value', 'Key1', 'Key2
+'],
    ['-' x 12, '-' x 12, '-' x 12],
    sort {$b->[0] <=> $a->[0]} 
    map {[$hash{$_->[0]}{$_->[1]}[0], @$_]} 
    map {my $key = $_; map {[$key, $_]} keys %{$hash{$_}}} keys %hash;

__DATA__
red           bike   
red           car    
red           shoes  
yellow        shoes  
yellow        skates
[download]

Prints:

Key1        Key2        Value       
------------------------------------
yellow      skates      5           
yellow      shoes       4           
red         shoes       3           
red         car         2           
red         bike        1
[download]