How would I use entity wrapper to insert new values into an entity property list? bundle?

A field can only hold multiple values if it's been explicitly set to hold more than one value (this is an option when creating the field - see "How many values the field will store" at http://drupal.org/documentation/modules/field-ui ). In that case, the correct syntax using the entity metadata wrapper is to use array operator [] as follow:

$tids = array(....);
$wrapper = entity_metadata_wrapper('node', node_load(1));
foreach ($tids as $tid) {
  $wrapper->field_taxonomy[] = $tid;
}

Please note that in your original example you use the field 'title' - however that is a special drupal field, and it cannot be made to be multi-valued.