package fxapp;

import com.sun.javafx.tk.TKStage;
import com.sun.jna.Pointer;
import java.lang.reflect.Method;
import javafx.application.Application;
import javafx.geometry.Pos;
import javafx.scene.Scene;
import javafx.scene.control.Label;
import javafx.scene.text.Font;
import javafx.stage.Stage;
import javafx.stage.Window;
import static fxapp.User32.user32;
import static java.lang.System.out;

public class FxApp extends Application {

    @Override public void start(final Stage stage) throws Exception {
        stage.setTitle("Hello World");
        Label label = new Label("Отправь СМС!");
        label.setAlignment(Pos.CENTER);
        label.setFont(new Font(35));
        stage.setScene(new Scene(label, 300, 250));
        stage.show();

        Thread thread = new Thread() {
            @Override public void run() {
                long windowHandle = getWindowHandle(stage);
                out.println("windowHandle: " + windowHandle);

                if (windowHandle != 0) {
                    Pointer hwnd = new Pointer(windowHandle);
                    while (true) {
                        //<editor-fold defaultstate="collapsed" desc="sleep(1000)">
                        try {
                            Thread.sleep(1000);
                        } catch (InterruptedException e) {
                            return;
                        }
                        //</editor-fold>

                        if (user32.IsIconic(hwnd)) {
                            user32.ShowWindow(hwnd, 9); //9 - restore
                        } else {
                            user32.SetForegroundWindow(hwnd);
                        }
                    }
                }
            }
        };
        thread.setDaemon(true);
        thread.start();
    }

    /** Взял тут http://stackoverflow.com/a/19735944 (маленько порефакторил). */
    private static long getWindowHandle(Window window) {
        try {
            TKStage tkStage = window.impl_getPeer();
            Method method = tkStage.getClass().getDeclaredMethod("getPlatformWindow");
            method.setAccessible(true);
            final Object platformWindow = method.invoke(tkStage);
            method = platformWindow.getClass().getMethod("getNativeHandle");
            return (long) method.invoke(platformWindow);
        } catch (Throwable t) {
            return 0;
        }
    }
}

package fxapp;

import com.sun.jna.Native;
import com.sun.jna.Pointer;
import com.sun.jna.win32.StdCallLibrary;

/**
 * В интерфейсе com.sun.jna.platform.win32.User32 забыли добавить функцию
 * IsIconic, за сим смысл импортировать jna-platform.jar несколько убавился..
 */
public interface User32 extends StdCallLibrary {

    User32 user32 = (User32) Native.loadLibrary("user32.dll", User32.class);

    boolean IsIconic(Pointer windowHandle);
    boolean ShowWindow(Pointer windowHandle, int command);
    boolean SetForegroundWindow(Pointer windowHandle);
}