Ok, with some help I found the code to add a new application / section without modifying the config manually. Add an assmebly with this class in the /bin folder and the section is automatically added to Umbraco.

    [Application("guestbook", "Guestbook", ".trayguestbook", 20)]
    public class Class1 : IApplication
    {

Then you can modify the Tree by adding a class that inherits from BaseTree.

    [Tree("guestbook", "guestbookTree", "Guestbook")]
    public class Class2 : BaseTree
    {

But now how do I modify the Dashboard? Is there a way to do this with code or is it config only?