One of the capabilities of CRM is to build a Web Resource which can help you expose a custom UI on CRM Forms or Dashboards. We can also use the web resources to call third party services and expose some interesting functionality in the web resource. This web resource can then be hosted in the CRM UI and call your WCF service to show interesting data. The problem though is how do you enable authentication on your WCF service.
CRM supports multiple authentication methods. If its an on premise installation it could be using AD, ADFS etc. for authentication. It could be an IFD deployment using a 3rd party authentication provider. If its CRM online it could be using Live authentication or authenticating using the federation with Office 365.
It becomes quite a task if the 3rd party provider has to provide a web resource and ensuring that they authenticate against every possible authentication mechanism that CRM could be using. I tried to get help from a few discussion groups and is a potential solution
Use a shared key to authenticate the callers of the service. Store this key in a CRM entity instance and use it every time (in the WCF header) you call the WCF service hosted on your server. This key can be stored at the time one buys the license to use your web resource. If you plan to impersonate the user then let every user have a different key and map them in a database on the WCF service side. With impersonation enabled the user provisioning headaches for the administrator will increase but at least you can achieve it.
Its not as elegant as we want it to be but it can definitely work. I would wait for CRM Online to support a single mode of authentication using Azure Active Directory to at least make it consistent in CRM online world. i.e. with every CRM online subscription you get a subscription of Azure Active Directory. And then your web resource can pass the token to WCF service hosted by you which can check with the Azure Active Directory for validity and do the job for you.
Hope this helps!!