I wonder is it possible to combine functionalities of both Force.com sites and Site.com pages. I know that I cannot use Visualforce pages / Apex code in Site.com, but is it possible to add reference from site.com site to Force.com site (for example I would like to add Force.com site as a menu option in Site.com site's menu).
You can not combine Force.com sites and Site.com together on a single page. Both have different structure. Site.com is like static page having some dynamic widgets to perform basic operations. You can navigate from site.com page to Force.com site visulaforce page but cannot mix them together.