Custom Themes & Templates

Merchants with a strong technical background and experience in template-based software, may be able to perform more extensive theme modifications.  Prior to taking on this level of design effort, it is important that merchants/developers have a solid understanding of the Magento template structure and fall-back hierarchy.

This article is a good starting point:

http://www.magentocommerce.com/design_guide/articles/how-magento-builds-content

Also, the articles below illustrates the Magento theme hierarchy.  Understanding how Magento uses templates is critical and this would be required reading for anyone looking to customize a template or build a custom theme:

http://www.magentocommerce.com/knowledge-base/entry/magentos-theme-hierarchy

http://code.tutsplus.com/articles/an-introduction-to-magento-design-terminology-and-concepts–cms-20644