Reusable pieces of a theme (mostly markup) should utilize http://codex.wordpress.org/Function_Reference/get_template_part
Allows for proper child theme's as well.
Are you able to put template_part files in in sub-directories? I don't see that in the documentation. get_template_part seems like it'd be a good idea, but I like separating things out and keeping my folders tidy.
Yup, should work fine using the $slug param: get_template_part('folder/file');
Hmm, doesn't seem to work so smoothly like that. It should, but it doesn't seem to...
I'm going to move to keeping template parts in a partials subfolder under includes, but I'm going to wait to move to get_template_part() until WordPress allows you to specify a directory, which I'm sure is only a matter of time.
Good decision. Looks like it should be added before 3.4 comes out: https://core.trac.wordpress.org/ticket/15086
Merged in jamie (pull request #2)
Updated readme with project setup notes.
Merge pull request #2 from eriku/master
Added menu_item_parents =  variable to sub_menu.php to stop array error