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
{
Is there a way to modify the dashboard with a similair approach as well?
Thanks!