I'm late to the party here, but thought i'd post what i was playing around with anyway...

#!/usr/bin/perl -w
use 5.012;

# Read in the header
my $hdr = <DATA>;
chomp $hdr;

my @lines;
my $line = 0;
my $column = -1;
my $previous_a = '';

while (<DATA>) {
        chomp;
        my ($a,$b,$c) = split;
        if ($a ne $previous_a) {
                $lines[0][++$column] = $hdr;
                $line = 1;
                $previous_a = $a;
        }
        $lines[$line++][$column] = $_;
}

$,="\t";
say map {defined($_) ? $_ : ''} (@$_) for (@lines);

__DATA__
a b c
0 0 d
0 1 d
0 1 d
0 2 d
0 2 d
1 0 d
1 0 d
1 1 d
1 1 d
1 2 d
1 2 d 
2 0 d
2 0 d
1 0 d
1 0 d
1 1 d
1 1 d
1 2 d
1 2 d
[download]

Produces:

a b c   a b c   a b c   a b c
0 0 d   1 0 d   2 0 d   1 0 d
0 1 d   1 0 d   2 0 d   1 0 d
0 1 d   1 1 d           1 1 d
0 2 d   1 1 d           1 1 d
0 2 d   1 2 d           1 2 d
        1 2 d           1 2 d
[download]