Same as with method insert(), it is worth noting that creating a reference to $obj will have the same effect as $obj being a reference itself, i.e. no _id field will be added.
<?php
$a = &$obj;
$m = new MongoClient;
$collection = $m->test->phpmanual;
$obj = array('x' => 1);
// Suppose you create a reference for some reason
$a = &$obj;
$collection->save($obj);
var_dump($obj);
// prints: array(1) { ["x"]=> int(1) }
?>