How to manipulate Drupal 7's fields, based on entity reference example. Minus validation, duplicates check, etc. Only the core logic. Please comment if you think it's substantially wrong.

gistfile1.php

$node = node_load($nid);
$node_wrapped = entity_metadata_wrapper('node', $node);
$references = $collection_node->[name_of_reference_field]->value();

// append new reference (note no sanity checks are included with this Gist)
$references[] = node_load($referenced_nid);

$collection_node->field_cards_reference->set($references);
$collection_node->save();