I came across a pain in the arse issue with SharePoint the other day but now I have managed to get around it, it was an issue where ASMX web services stopped working completely.
The Symptoms when trying to use an ASMX with SharePoint and .Net 3.5
Page: “An error has occurred on the server”
SharePoint Log:“Application error when access /_vti_bin/Lists.asmx, Error=Failed to Execute URL.”
Fiddler: HTTP 401 Unauthorized
I managed to track the issue down to the ordering of the HTTPHandlers in the Web.config, it has added the remove of the ASMX to the bottom!
<httpHandlers>
<remove verb="GET,HEAD,POST" path="*" />
<add verb="GET,HEAD,POST" path="*" type="Microsoft.SharePoint.ApplicationRuntime.SPHttpHandler, Microsoft.SharePoint, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<add verb="OPTIONS,PROPFIND,PUT,LOCK,UNLOCK,MOVE,COPY,GETLIB,PROPPATCH,MKCOL,DELETE,(GETSOURCE),(HEADSOURCE),(POSTSOURCE)" path="*" type="Microsoft.SharePoint.ApplicationRuntime.SPHttpHandler, Microsoft.SharePoint, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<add verb="*" path="Reserved.ReportViewerWebControl.axd" type="Microsoft.Reporting.WebForms.HttpHandler, Microsoft.ReportViewer.WebForms, Version=8.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" />
<add verb="*" path="*.asmx" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="*" path="*_AppService.axd" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="GET,HEAD" path="ScriptResource.axd" type="System.Web.Handlers.ScriptResourceHandler, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" validate="false" />
<remove verb="*" path="*.asmx" />
</httpHandlers>
Should be
<httpHandlers>
<remove verb="GET,HEAD,POST" path="*" />
<remove verb="*" path="*.asmx" />
<add verb="GET,HEAD,POST" path="*" type="Microsoft.SharePoint.ApplicationRuntime.SPHttpHandler, Microsoft.SharePoint, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<add verb="OPTIONS,PROPFIND,PUT,LOCK,UNLOCK,MOVE,COPY,GETLIB,PROPPATCH,MKCOL,DELETE,(GETSOURCE),(HEADSOURCE),(POSTSOURCE)" path="*" type="Microsoft.SharePoint.ApplicationRuntime.SPHttpHandler, Microsoft.SharePoint, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<add verb="*" path="Reserved.ReportViewerWebControl.axd" type="Microsoft.Reporting.WebForms.HttpHandler, Microsoft.ReportViewer.WebForms, Version=8.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" />
<add verb="*" path="*.asmx" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="*" path="*_AppService.axd" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="GET,HEAD" path="ScriptResource.axd" type="System.Web.Handlers.ScriptResourceHandler, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" validate="false" />
</httpHandlers>