Nel caso in cui tu abbia davvero bisogno che sia ordinato ora senza riprogettare il tuo database (cosa che vorrei)...
$ids = array(1,2,4);
$query = "SELECT room_location.*, client_room.*, users.* FROM room_location INNER JOIN client_room ON room_location.user_loc_id = client_room.id INNER JOIN users ON room_location.user_loc_id = users.userGroupLocID WHERE userGroupLocID REGEXP '(^|,)(".implode('|',$ids).")(,|$)' ORDER BY room_location.location";