You can launch the application with gksudo to start it in super-user mode, e.g. to start Tomboy issue the command gksudo tomboy. You'll be presented with a graphical password prompt and after you enter correct password the application will be started in super-user(root) mode.

However, if you want to change this behaviour in the Application Menu then you have to change the Exec= line of the .desktop file corresponding to the application by adding gksudo after Exec= .i.e. Exec=gksudo tomboy. You can also do it using alacarte or Menu Editor, just find the right application menu-item, go to Properties and edit its Command field and add a gksudo before whatever is there.