If there's a lot of links to the homepage, which structure would let its pages rank higher? site.com/index.php?go=layouts&q=christmas site.com/layouts/code/christmas.html?
I would use the second link, when given the chance always keep your links static and not dynamic. Static links are better for your overall SEO. Keep in mind what anchor text you use on those links will help out as well.
Go for the second link... SE friendly and easily be crawled by SE... If you choose the number 1 you will url-rewrite it in the future...