Hi,
I just released a new video course on how to create a Wordpress theme/template from scratch.
About the video:
Video Synopsis - Building a Simple WordPress Theme
In these 12 videos, we will take someone with some beginner HTML and CSS skills through the steps needed to build a WordPress template from scratch. The videos use only a [...]

In the following podcast I go over the key factor when determining how to structure a PHP project.
In a nutshell, it comes down to the size and complexity of the job. For the details, listen to me yap:
php-podcast-project-structure
Thanks,
Stefan Mischook
www.killerphp.com