The functions.php file is the heart of your theme yet it’s almost always the longest and most unorganized file in most themes. This talk will cover the reasons to keep it clean and organized such as extensibility, open sourcing, code reuse and bug fixes. Treat your theme with care and make it easy to share with a few simple strategies. Freelancers and professionals alike can benefit from this session on “heart healthy” theme development.
Slide: http://prezi.com/yl4x6et37erm/better-theme-organization-brent-schultz-at-2014-kc-wordcamp