As a designer at <a href="http://www.flugpo.com">Flugpo</a> I deal with this problem all the time.
With CSS I really think the best answer is one monolithic CSS file. Add a index at the top and keep it organized by global, section and page: http://www.flugpo.com/FlugPo/styles/style.css
With JS I find breaking it down by section files alone with one global file to be the best way to approach it.
Comments
As a designer at <a href="http://www.flugpo.com">Flugpo</a> I deal with this problem all the time.
With CSS I really think the best answer is one monolithic CSS file. Add a index at the top and keep it organized by global, section and page: http://www.flugpo.com/FlugPo/styles/style.css
With JS I find breaking it down by section files alone with one global file to be the best way to approach it.