If you are passing $_GET parameters to your queries, make sure that they are cast to strings first. Users can insert associative arrays in GET requests, which could then become unwanted $-queries.
A fairly innocuous example: suppose you are looking up a user's information with the request http://www.example.com?username=bob. Your application does the query $collection->find(array("username" => $_GET['username'])).
Someone could subvert this by getting http://www.example.com?username[$ne]=foo, which PHP will magically turn into an associative array, turning your query into $collection->find(array("username" => array('$ne' => "foo"))), which will return all users not named "foo" (all of your users, probably).
This is a fairly easy attack to defend against: make sure $_GET's parameters are the type you expect before you send them to the database (cast them to strings, in this case).
Thanks to » Phil for pointing this out.