This is what I get with your code (and this is expected):
-------------------
array(2) {
  ["id"]=>
  string(1) "1"
  [0]=>
  string(1) "1"
}

Fatal error: Uncaught exception 'PDOException' with message 'SQLSTATE[HY000]: General error: 2014 Cannot execute queries while other unbuffered queries are active.  Consider using PDOStatement::fetchAll().  Alternatively, if your code is only ever going to run against mysql, you may enable query buffering by setting the PDO::MYSQL_ATTR_USE_BUFFERED_QUERY attribute.' in /tmp/1.php:11
Stack trace:
#0 /tmp/1.php(11): PDO->prepare('SELECT id FROM ...')
#1 {main}
  thrown in /tmp/1.php on line 11
-------------------

OK, so change the fetches for fetchAlls an alter the expected and actual results acordingly (yes I have tested with those methods). The bug still stands. Prepared statements are not working for this install.

It still doesn't work without execute() after prepare().
And after adding this execute() call, it works _just fine_.

Ahh, sorry, little typo, OK it looks like it's just in the parameter insertion then (do I need to start a new bug report?)

Revised Code
------------
<?php
//phpinfo();

$db   = new PDO('mysql:host=localhost;dbname=test', 'root', '');
$db->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
$stmt = $db->prepare("SELECT id FROM recipe WHERE id=?");
$stmt->bindValue(1, 1);
$stmt->execute();
$res = $stmt->fetchAll();
var_dump($res);

$stmt = $db->prepare("SELECT id FROM recipe WHERE id=1");
$stmt->execute();
$res  = $stmt->fetchAll();
var_dump($res);

foreach($db->query("SELECT id FROM recipe WHERE id=1") as $res) {
    var_dump($res);
}

Expected Result
---------------
array(1) {
  [0]=>
  array(2) {
    ["id"]=>
    string(1) "1"
    [0]=>
    string(1) "1"
  }
}
array(1) {
  [0]=>
  array(2) {
    ["id"]=>
    string(1) "1"
    [0]=>
    string(1) "1"
  }
}
array(2) {
  ["id"]=>
  string(1) "1"
  [0]=>
  string(1) "1"
}

Actual Result
-------------
array(0) {
}
array(1) {
  [0]=>
  array(2) {
    ["id"]=>
    string(1) "1"
    [0]=>
    string(1) "1"
  }
}
array(2) {
  ["id"]=>
  string(1) "1"
  [0]=>
  string(1) "1"
}

Please try using this CVS snapshot:

  http://snaps.php.net/php5.1-latest.tar.gz
 
For Windows:
 
  http://snaps.php.net/win32/php5.1-win32-latest.zip

I get the following error when doing the make install

SECURITY ERROR: PHP_Archive::mapPhar can only be called from within the phar that initiates itInstalling PDO headers:          /usr/local/php/include/php/ext/pdo/


Also earlier in the make install I get the following libtool warning
libtool: install: warning: remember to run `libtool --finish /usr/local/src/php5.1-200603200930/libs'

Discovered that I can still use php but I'm still getting the same result

array(0) {
}
array(1) {
  [0]=>
  array(2) {
    ["id"]=>
    string(1) "1"
    [0]=>
    string(1) "1"
  }
}
array(2) {
  ["id"]=>
  string(1) "1"
  [0]=>
  string(1) "1"
}

Ignore them. I believe you don't need PEAR to test PDO.

No feedback was provided for this bug for over a week, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".