For example, let's say you want to define an add-in model, or provide some base forms so my customers can extend to customize the look-and-feel of my app by just dropping in additional assemblies. How can you achieve this with "ClickOnce"?
You can build whatever customization mechanism you would normally build into your application. The only aspect that really changes with "ClickOnce" is the need to author manifests. Once a customer has created a customized version of your application, they can simply update your original "ClickOnce" application and deployment manifests to include the new files and resign with their own key. This can be done the MAGE tool.