use strict;
use warnings;

my @data;
while (<DATA>) {
   chomp;
   push @data, [ split /\s+|,/ ];
}

@data = sort {  $a->[0] cmp $b->[0]
             || $a->[1] <=> $b->[1]
             }
        @data;

my %order;
my $last_f;
my $last_x;
for (@data) {
   if (!defined($last_f) || $last_f ne $_->[0]) {
      $order{$_->[0]}{$_->[1]} = +1;
      $last_f = $_->[0];
      $last_x = $_->[1];
   }

   if ($last_x ne $_->[1]) {
      $order{$_->[0]}{$_->[1]} = -$order{$last_f}{$last_x};
      $last_x = $_->[1];
   }
}

@data = sort {    $a->[0] cmp $b->[0]
             ||   $a->[1] <=> $b->[1]
             || ( $a->[2] <=> $b->[2] ) * $order{$a->[0]}{$a->[1]}
             }
        @data;

print("$_->[0] $_->[1],$_->[2]\n") for @data;

__DATA__
...

##</code><code>##

use strict;
use warnings;

my %data;
while (<DATA>) {
   chomp;
   my ($f,$x,$y) = split /\s+|,/;
   push @{ $data{$f}{$x} }, $y;
}

my @data;
my $order = +1;
for my $f (sort keys %data) {
   my $xs = $data{$f};
   for my $x (sort { $a <=> $b } keys %$xs) {
      my $ys = $xs->{$x};
      push @data, map [ $f, $x, $_ ],
                  sort { $order * ( $a <=> $b ) }
                  @$ys;
      $order *= -1;
   }
}

print("$_->[0] $_->[1],$_->[2]\n") for @data;

__DATA__
...

##</code><code>##

aaa 1,2
aaa 2,1
aaa 2,3
aaa 3,1
aaa 3,2
aaa 4,1
aaa 4,5
bbb 2,2
bbb 2,5
bbb 2,1
bbb 4,3
bbb 4,6
bbb 4,1
bbb 4,2
ccc 3,3
ccc 3,6
ccc 1,3
ccc 1,1
ccc 6,4
ccc 6,6
ccc 2,2
ccc 2,4