First we create a file, mysite.info:
name = mysite
description = Various functions and files required by mysite.com
core = 7.x
package = Other
; Uncomment and expand the following lines as required.
; Files containing classes
;files = mysite.inc
;stylesheets[all] = mysite.css
;scripts = mysite.js
We also create a file, mysite.module, containing any site-specific php code which might be necessary. The most common function in this module is mysite_cron(), which implements any special maintenance tasks necessary for the site to function. Even if you do not have any site-specific functions, place an empty mysite.module file in the modules/mysite directory so your module can be activated under admin/modules.
* Add any site specific tasks and hook implementations below.
The sky is the limit here, but the intent of this method is to create a repository of all those little odds and ends you include in any site development.
If you are developing a major function for your site, you are advised to do it in its own module, and perhaps put it up on the Drupal site, as others may have an interest in it. That way you have the whole community testing, coding, proposing upgrades, etc.