Some hosts place your web site under a subdirectory on the server. For example, while GitHub Pages puts user and organization sites at a root "http://username.github.io" URL, it serves project sites as "http://username.github.io/repository". It's easy to support these kinds of deployments with a couple settings in Wyam.
To make all generated links use the subdirectory name, place the following at the top of your configuration file and set the appropriate subdirectory:
Settings[Keys.LinkRoot] = "/subdirectory";
That will result in all the links that were created using IExecutionContext.GetLink() having the correct subdirectory. While the recipes and themes are designed to automatically support this convention, you may need to make changes to your own files or custom generation logic to take advantage of the setting. Make sure that all of the links you specify without using the GetLink() method point to the correct relative URL with the subdirectory.
While the setting above controls generation, it does not impact serving the site with the preview server. To test how the site will work when a host is serving it under a subdirectory, use the --virtual-dir "/subdirectory" option when running via the command line. This will tell the preview web server to serve your site under the specified virtual directory. You almost always want to use this preview server setting in conjunction with the generation setting above to both generate and preview the site under the desired virtual directory.