<?php
$total = Array(
    'one' => Array(
            'value' => 158,
            'percent' => 38.73
        ),
    'two' => Array(
            'value' => 129,
            'percent' => 31.62
        ),
    'three' => Array(
            'value' => 121,
            'percent' => 29.66
        ),
    'all' => 408
);
$total['three']['percent'] = 100-($total['one']['percent']+$total['two']['percent']);
if($total['three']['percent'] < 0 && $total['two']['percent'] > 0-$total['three']['percent']){
    $total['two']['percent'] += $total['three']['percent'];
    $total['three']['percent'] = 0;
}else if($total['three']['percent'] < 0){
    $total['one']['percent'] += $total['three']['percent'];
    $total['three']['percent'] = 0;
}
print_r($total);
?>

Array
(
    [one] => Array
        (
            [value] => 158
            [percent] => 38.73
        )

    [two] => Array
        (
            [value] => 129
            [percent] => 31.62
        )

    [three] => Array
        (
            [value] => 121
            [percent] => 29.65
        )

    [all] => 408
)