While working on large Drupal installations theme folders can get very large. If you have numerous whatever.tpl.php files it can become quite confusing to locate the template file you need to edit when you need to make a change to your site. On top of that, if you are adding a lot of additional variables through pre-process functions (you are doing this in preprocess functions right, not in the tpl's...) your template.php file can become quite large as well. To remedy this there are two very simple things you can do to help organize your files and develop a theme structure that is much easier to maintain.
