$list = array(
    1 => array(
        'id' => 1,
        'parent' => 0
    ),
    2 => array(
        'id' => 2,
        'parent' => 0
    ),
    3 => array(
        'id' => 3,
        'parent' => 2
    ),
    4 => array(
        'id' => 4,
        'parent' => 2
    ),
    5 => array(
        'id' => 5,
        'parent' => 2
    ),
    6 => array(
        'id' => 6,
        'parent' => 5
    ),
);

foreach ($list as $id => &$leaf) {
    if ($leaf['parent'] !== 0) {
        $list[$id]['children'][] = &$leaf;
    }
}

echo "<pre>"; print_r($list); echo "</pre>";