Hi I personally would host them in a subfolder - especially the PDFs as they are likely to gain links and these links will help strengthen your domain.
However if you have them in a sub-domain they won't have the same benefit from the links as Google essentially treats sub-domains as a separate domain. This will also limit the ranking ability of PDFs as they won't benefit from your domains authority on a sub-domain.
Have a look at this article for a bit more insight into subfolder vs sub-domain
- http://www.seomoz.org/blog/understanding-root-domains-subdomains-vs-subfolders-microsites
I hope this helped..


