Personalization is an issue with my first mix of a web service on my DNN server.
DNN turns Personalization ON (new ASP.NET 2.0 feature), and if your web service application isn't coordinated with this, then it will not run on the same Web Site.
You can create a new web site, then change its port to something other than the DNN port (80), for example 8088, and then you can add the virdir for the web service. You can reach the web service with the usual domain name for your DNN site with the colon + port # you've chosen, e.g. http://myDNNsite.com:8088/
http://msdn.microsoft.com/library/default.asp?url=/library/en-us/cpgenref/html/gngrfaddforprotocols.asp
This link will show you that to enable the 'test' button on the web service test page, you need add lines to your web.config as described, i.e.
The following example enables all four currently supported protocols.
<configuration>
<system.web>
<webServices>
<protocols>
<add name="HttpSoap"/>
<add name="HttpPost"/>
<add name="HttpGet"/>
<add name="Documentation"/>
</protocols>
</webServices>
</system.web>
</configuration>
HTH
I have not yet tried turning Personalization on for my test web service, but I think this must be done correctly to embed a service in any DNN module.