The following quick SDK sample demonstrates how to list and change the managed runtime version of application pools programatically in IIS 7.

[VB]

Imports System
Imports Microsoft.Web.Administration
Public Class AppPoolSample
 Shared manager As ServerManager = New ServerManager()
  ' Main application processing
  Public Shared Sub Main(ByVal args As String())
      ' Get the apppool to change
      Dim iPool As Integer = GetAppPool()
      ' Get the framework version desired
      Dim rtVersion As String = GetVersion()
      ' Set the apppool runtime
      Dim poolToSet As ApplicationPool = manager.ApplicationPools(iPool)
      Console.WriteLine(
            "Setting application pool '{0}' to runtime version: {1}...", _
            poolToSet.Name, rtVersion)
      poolToSet.ManagedRuntimeVersion = rtVersion
      ' Commit the changes and recycle the application pool
      manager.CommitChanges()
      poolToSet.Recycle()
      Console.WriteLine("Your changes have been committed.")
  End Sub

  ' Prompts the user to select an application pool
  Public Shared Function GetAppPool() As Integer
    Dim pool As String = String.Empty
    Dim iPool As Integer = 0
    While (Not Integer.TryParse(pool, iPool))
      Console.WriteLine("Available ApplicationPools: Managed runtime version")
      Dim i As Integer
      For i = 0 To manager.ApplicationPools.Count - 1 Step i + 1
        Dim appPool As ApplicationPool = manager.ApplicationPools(i)
        Console.WriteLine("{3}{0,3}.{3}{1}: {2}", i + 1, _
            appPool.Name, appPool.ManagedRuntimeVersion, vbTab)
      Next
      Console.Write("{0}Choose an application pool to change: ", vbCrLf)
      pool = Console.ReadLine()
    End While
    Return iPool - 1
  End Function

    ' Prompts a user to select the version of runtime they would like
    ' the application pool to use
    Public Shared Function GetVersion() As String
        Dim rtVersion As String = String.Empty
        Dim iVersion As Integer = 0
        While (Not Integer.TryParse(rtVersion, iVersion))
            Console.WriteLine("{0}  1.{0}Framework version 1.0", vbTab)
            Console.WriteLine("{0}  2.{0}Framework version 1.1", vbTab)
            Console.WriteLine("{0}  3.{0}Framework version 2.0", vbTab)
            Console.Write("Choose the new managed runtime version: ")
            rtVersion = Console.ReadLine()
        End While
        Select Case iVersion
            Case 1
                rtVersion = "v1.0"
            Case 2
                rtVersion = "v1.1"
            Case 3
                rtVersion = "v2.0"
        End Select
        Return rtVersion
    End Function
End Class

[C#]

using System;
using Microsoft.Web.Administration;

public class AppPoolSample 
{
  static ServerManager manager = new ServerManager();
  // Main application processing
  public static void Main(string[] args)  
  {
    // Get the apppool to change
    int iPool = GetAppPool();
    // Get the framework version desired
    string rtVersion = GetVersion();
    // Set the apppool runtime
    ApplicationPool poolToSet = manager.ApplicationPools[iPool];
    Console.WriteLine(
        "Setting application pool '{0}' to runtime version: {1}...",
        poolToSet.Name, rtVersion);
    poolToSet.ManagedRuntimeVersion = rtVersion;
    // Commit the changes and recycle the application pool
    manager.CommitChanges();
    poolToSet.Recycle();
    Console.WriteLine("Your changes have been committed.");
  }
  // Prompts the user to select an application pool
 public static int GetAppPool()
 {
    string pool = String.Empty;
    int iPool = 0;
    while ((!int.TryParse(pool, out iPool)) ||
            (iPool > manager.ApplicationPools.Count || iPool <= 0))
    {
      Console.WriteLine(
                    "Available ApplicationPools: Managed runtime version");
      for (int i = 0; i <= manager.ApplicationPools.Count - 1; i++)
      {
        ApplicationPool appPool = manager.ApplicationPools[i];
        Console.WriteLine("t{0,3}.t{1}: {2}", i + 1, 
            appPool.Name, appPool.ManagedRuntimeVersion);
      }
      Console.Write("rnChoose an application pool to change: ");
      pool = Console.ReadLine();
  }
  return iPool -1;
}
  // Prompts a user to select the version of runtime they would like
  // the application pool to use
  public static string GetVersion()
  {
    string rtVersion = String.Empty;
    int iVersion = 0;
    while ((!int.TryParse(rtVersion, out iVersion)) ||
            (iVersion > 3 || iVersion < 1))
    {
      Console.WriteLine("rnt   1.tFramework version 1.0");
      Console.WriteLine("t   2.tFramework version 1.1");
      Console.WriteLine("t   3.tFramework version 2.0");
      Console.Write("Choose the new managed runtime version: ");
      rtVersion = Console.ReadLine();
    }
    switch (iVersion)
    {
        case 1:
            rtVersion  = "v1.0";
            break;
        case 2:
            rtVersion = "v1.1";
            break;
        case 3:
            rtVersion = "v2.0";
            break;
    }
    return rtVersion;
  }
}