Organizing common functions/classes
In your .module file add the following to the very top of the module (just after the opening &lt;?php tag):

module_load_include('inc', 'common', 'common.query');
module_load_include('inc', 'common', 'common.taxonomy');


For your reference:

module_load_include();

EDIT

Seeing as how you're not going to be needing these on cached pages, then putting them in hook_init() is much better practice.

Like the following:

function common_init() {
  module_load_include('inc', 'common', 'common.query');
  module_load_include('inc', 'common', 'common.taxonomy');
}