How do I theme my module output (specifically the nodes coming out of EntityFieldQuery)?
Instead of doing a full node view you can make a custom node view like

return node_view_multiple($nodes, 'module_name');


That will enable you to create custom logic for this view type and setup field display as well if needed.

To define your own view mode you need to add it using hook_entity_info_alter

/**
 * Implements hook_entity_info_alter().
 */
function hook_entity_info_alter(&amp;$entity_info) {
  $entity_info['node']['view modes']['module'] = array(
    'label' =&gt; t('Name'),
    'custom settings' =&gt; TRUE,
  );
}