The Model-View-Controller (or as @bmf calls it, Data-user-Logic) is a good starting point for a GUI application (and honestly, even or the command line).

Separate what you're working on and the code that manages that (the model) from the code that puts something on the screeen (the view), and create code that pulls data from the model, does something to it, and either puts it back or shows some of it to the user (the view).

Being strict about this can make the whole thing lots easier. The controller code turns mostly into code to move data from point A to point B, maybe changing what it's kept in during the process. The view takes very simple sets of data and shows them. The model provides easy ways to get the data from your files/database/network into a data structure that the controller can use.