Organizing common functions/classes Currently I have a common.module for storing common functions.  This file is getting way to long and I'd like to start breaking it up by similar functionality or by class:

common.inc
common.query.inc
common.taxonomy.inc
Node.php
etc...


I thought I could add files[] entries to my common.info file but this doesn't seem to source these files.

I need these files to be always sourced: on any page load, on full drupal bootstrap, and on update.php.
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');
}