Let Tie::IxHash keep your order.
I did not understand which order is prefered for your example, but put them in your order into the hash. That's what you get back.
my @array1 = (1, 3, 4, 6);
my @array2 = (1, 2, 4, 6);
my @array3 = (1, 2, 3, 5);
tie my %seen, 'Tie::IxHash';
for (0..$#array1) {
my @v = sort ( $array1[$_], $array2[$_], $array3[$_] );
@seen{ @v } = 1;
}
print join ' ', keys %seen;
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