SharePoint is a lot more than just an ASP.Net web application. It is primarily an object model, within this there are many methods, classes and handlers, which are best accessed by way of the WCF web services.
Accessing SharePoint can be achieved through HTTPWebRequest / Response methods. I would suggest this creates a static link by the URL, which may not suit the requirement. For this reason you can use the SharePoint Web Service to enumerate sites, sub-sites and contents.
The Lists Web service provides methods for working with SharePoint lists, content types, list items, and files. Access this Web service, by creating a Web reference to http://site/_vti_bin/Lists.asmx
This is only one aspect of the available services, refer to MSDN for more.