Another issue that may be faced when deploying custom .Net applications in the CRM root directory is the following error:
'Microsoft.Crm.WebServices.Crm2007.MultipleOrganizationSoapHeaderAuthenticationProvider,
Microsoft.Crm.WebServices, Version=4.0.0.0, Culture=neutral,
PublicKeyToken=31bf3856ad364e35' doesn't exist.
You can resolve this one of two ways...
1. Add the following to your applications web.config (not CRM's web.config!)
<assemblies>
<clear/>
<add assembly="*"/>
</assemblies>
2. Go to the crm bin directory for IIS and either copy the Microsoft CRM.WebServices.dll to the GAC or to the bin directory of your custom ASP.Net application