And write with big letters "references are NOT pointers!" :)

Also, as I've discovered in further testing, even 
internal references are not preserved when serialize() 
and unserialize() are employed. For instance (mind the 
pun, it's tricky): 

Sample Code:
============

class A {
  var $value = 0;

  function A ( $newValue = 0 ) {
    $this->value = $newValue;
  } // END constructor
} // END class A

class B {
  var pointers = array(); 
  vae aliases = array();
  // Excuse the misnomers, please...

  function B ( $newPointer = false ) {
    if (false !== $newPointer) 
      $this->ponters[] =& $newPointer;
    foreach ($pointers as $index => $value)
      $this->aliases[$index] =& $pointers[$index];
  } // END constructor
} // END class B

$newA = new A('I'm a new A'); 
$newB = new B(&$newA);
$oldB = unserialize(serialize($newB));
$newA->value = "Now I'm an old A";

// Forgive the PHP5-style syntax below...

echo $newA->value; 
// As expected, Output: Now I'm an old A

echo $newB->pointer[0]->value;
// As expected, Output same...

echo $oldB->pointers[0]->value;
// Somewhat expected, but not desired...
// Output: I'm an old A

$oldB->pointers[0]->value = "Also an old A";
echo $oldB->pointers[0]->value;
echo $oldB->aliased[0]->value;
// Nothing as expected or desired...
// Output 1: Also an old A
// Output 2: I'm an old A
// Internal references aren't even preserved... Boo.

I fail to see the specific link with objects, nor the dilemnia, because serialize/unserialize can't keep references at all:

$a = 'first';
$b = &$a; // create a reference
$c = serialize($b);
unset($b); // kill the reference
$b = unserialize($c); // won't restore it, unserialize() doesn't return a reference.
$a = 'second';
echo $b;
-> 'first'

Well, as a second though, I would agree that the manual isn't clear enough. 

"References inside the array/object you are serialize()ing will also be stored."

$a = 'first';

$b = array(&$a);

$c = serialize($b);
unset($b);

$b = unserialize($c);
$a = 'second';

echo $b[0]; // -> first, which is not the behavior somebody would expect

This bug has been fixed in the documentation's XML sources. Since the
online and downloadable versions of the documentation need some time
to get updated, we would like to ask you to be a bit patient.

Thank you for the report, and for helping us make our documentation better.