With Moodle 2: I would suggest to use REST protocol or XML-RPC protocol. I don't think SOAP will work with .NET for the same reason as it doesn't fully work with JAVA: MDL-28988 and MDL-28989
We have some JAVA demo clients for REST/XML-RPC protocols: https://github.com/moodlehq/sample-ws-clients
.Net clients should be similar.
If someone tackles the issues mentioned above, I'll peer review them with pleasure.