If you want to build your own custom Web services that will be hosted in a sharepoint instance, here is the complete walkthrough that you need to folow:
MSDN Article: http://msdn.microsoft.com/en-us/library/ms464040.aspx
The tip is on step 12: if you didn't specify the assemblyname.classname you will not be able to successfully deploy your webservice.
Step 12 has to be :
WebService Language="C#" Class="MyServiceAssembly.Service, MyServiceAssembly, Version=126.96.36.199, Culture=neutral, PublicKeyToken=8f2dca3c0f2d0131"
That's is and hope it helps.