How do I get the handle of a console application's window

Try this:

[DllImport("user32.dll", EntryPoint = "FindWindow", SetLastError = true)]
public static extern IntPtr FindWindowByCaption(IntPtr zeroOnly, string lpWindowName);
…

Console.Title = "Test";
…

IntPtr handle = FindWindowByCaption(IntPtr.Zero, Console.Title);

One more version in VB.Net on how to show MessageBox on top of console window

Imports System.Runtime.InteropServices
Imports System.Windows.Forms

Friend Module NativeMethods
    <DllImport("kernel32.dll")> Friend Function GetConsoleWindow() As IntPtr
    End Function
End Module

NotInheritable Class WndProxy
    Implements IWin32Window
    ReadOnly Property Handle As IntPtr Implements IWin32Window.Handle
    Sub New(_hwnd As IntPtr)
        Handle = _hwnd
    End Sub
End Class

Module Module1

    Sub Main()
        ' using MainWindowHandle
        Dim w = New WndProxy(Process.GetCurrentProcess().MainWindowHandle)
        MessageBox.Show(w, "Hi")
        ' using GetConsoleWindow api
        Dim s = New WndProxy(NativeMethods.GetConsoleWindow)
        MessageBox.Show(s, "Hi")
    End Sub

End Module