SWT Application is very basic template with empty Shell, where you can add controls, like viewers, main menu, toolbat, etc. But you have to manage all items in menu and toolbar by hands.
In JFace ApplicationWindow you can also design content of window, but you can also swtich to "actions" tab in Designer, create set of actions and add them to MenuManager and ToolbarManager. So, your logic will be bound to actions that are place in menu and toolbar, and you can handle it selection and enable/disable them in single point - in your action.
We have good demo for ApplicationWindow: