<p>Is there a way to configure a Visual Studio 2005 Web Deployment Project to install an application into a named Application Pool rather than the default app pool for a given web site?</p>

There is a good article describing custom actions here:
ScottGu's Blog
The question you asked is answered about halfway through the comments by 'Ryan', unfortunately it's in VB, but it shouldn't be hard to translate:
```
```
Private Sub assignApplicationPool(ByVal WebSite As String, ByVal Vdir As String, ByVal appPool As String)
   Try
     Dim IISVdir As New DirectoryEntry(String.Format("IIS://{0}/W3SVC/1/Root/{1}", WebSite, Vdir))
     IISVdir.Properties.Item("AppPoolId").Item(0) = appPool
     IISVdir.CommitChanges()
   Catch ex As Exception
     Throw ex
   End Try
 End Sub

 Private strServer As String = "localhost"
 Private strRootSubPath As String = "/W3SVC/1/Root"
 Private strSchema As String = "IIsWebVirtualDir"
 Public Overrides Sub Install(ByVal stateSaver As IDictionary)
   MyBase.Install(stateSaver)
   Try
     Dim webAppName As String = MyBase.Context.Parameters.Item("TARGETVDIR").ToString
     Dim vdirName As String = MyBase.Context.Parameters.Item("COMMONVDIR").ToString
     Me.assignApplicationPool(Me.strServer, MyBase.Context.Parameters.Item("TARGETVDIR").ToString, MyBase.Context.Parameters.Item("APPPOOL").ToString)
   Catch ex As Exception
     Throw ex
   End Try
 End Sub
```
```
...Where APPPOOL is supplied as an argument in the Custom Action.