@Johan:

Well, there is this if you’re starting something new:
https://aarontgrogg.com/2010/10/06/my-first-wp-theme-boilerplate-starkers/

Or this if you want to “fine tune” an existing Theme:
https://aarontgrogg.com/2011/04/21/my-first-wordpress-plug-in-html5-boilerplate/

I almost recommend the plug-in over the theme, I think it is more flexible, but you can go your own way!

Cheers,
Atg