nathansh.com site functionality plugin
Custom post types and taxonomies, as well as other functionality pieces, should exist in a plugin, not a WordPress theme. This is to allow better portability through a separation of concerns. This plugin does just that for nathansh.com, and was build upon a boilerplate I maintain for the very purpose: github.com/domain7/wp-plugin_boilerplate.
Feel free to poke around, see how things are done, tweet me any questions @_nathansh, and if you're feeling adventurous make a pull request.
You might also be interested in the WordPress theme used for nathansh.com