Search engines places greater value on pages towards the root of your domain, with pages at the root level being percieved as the most relevant.
/important-page.html /folder/sub-folder/less-important-page.html
Because of this, you should aim to make your site folder structure as flat as possible.
Subdomains and subdirectories - mattcutts.com Flat Site Architecture is SEO-Friendly - bigoakinc.com Do Deep Folders Stop Search Engines? - allthingssem.com