@stevebak: The .references-folder is just a shorthand for not having to include references in all files. Still, you are free to additionally or only use ///-references in your files, e.g. /// <reference path="node.d.ts" />; those paths are always resolved relative to the file they are in.
Also, please note that with the next release of VSO Monaco we will support _references.ts files, instead of the .references-folder. These files are supposed to have ///-references only and are automatically added as dependency to sibling and descendent files.