Creating a Transparent Stage works fine on OS X Mavericks, but the stage is not Mouse-Transparent, so the scene rectangle blocks all mouse events from reaching applications behind (z-order) the JavaFX app. If I recall correctly this used to work in earlier versions, and also works on Windows.

This is true even if I make the parent non-rectangular:

@Override
    public void start(Stage primaryStage) {
        Circle circle = new Circle(100,100,100);
        StackPane root = new StackPane();
        root.getChildren().add(new Button("Hallo"));
        Scene scene = new Scene(root, 200, 200);
        root.setShape(circle);
        primaryStage.setScene(scene);
        primaryStage.initStyle(StageStyle.TRANSPARENT);
        scene.setFill(Color.TRANSPARENT);
        primaryStage.show();
    }

Expected behaviour:

Mouse events inside the scene rectangle but outside the circle in the four corners should go through to the application below the JavaFX app

Perceived Behaviour:

MouseEvents don't go through.