I recently been working on customizing CRM plug-in deployment tool to add some additional functionality. The source for the tool is available with the CRM 4.0 SDK.
To successfully build the source we need to add a web reference back to the CRM web service. The problem I ran into was that the default url (http://<server:port>/mscrmservices/2007/CrmServiceWsdl.aspx) returns a wsdl scheme with all its customizations. If you just need a clean proxy like I did then you need to create a new organization and then provide its name in the uniquename query string variable:
http://<server:port>/MSCrmServices/2007/CrmServiceWsdl.aspx?uniquename=OrganizationName
