This may be slightly more readable. Since it accesses elements of both arrays in the same way (using an index), it is a bit more consistent. It also eliminates the explicit $i++;. You can decide if it is better.

print "BEST        SELECTED BEST\n";
foreach my $value (sort keys %{$best}) {
    foreach my $i (0 .. $#{$best->{$value}}) {
        printf "%10.5f ", $best     ->{$value}[$i];
        printf "%10.5f" , $kept_best->{$value}[$i]
            if defined    $kept_best->{$value}[$i];
        print "\n";
    }
}
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