First you need to prevent app appear in taskbar
{
    "name": "My App",
    "version": "1.0.0",
    "main": "app.html",
    "window": {
        "show": false,
        "show_in_taskbar": false
    }
}
Then you need to create tray (top bar) menu: (example from his source)
tray = new app.node.gui.Tray({
    title: '',
    icon: 'assets/css/images/menu_icon.png',
    alticon: 'assets/css/images/menu_alticon.png',
    iconsAreTemplates: false
});
Then need create hidden window and show it on click in tray:
// create window
var params = {toolbar: app.devMode, frame: false, transparent: true, resizable: false, show: false};
window = app.node.gui.Window.open('templates/panel.html', params);
function showPopup (x, y) {
  window.on('document-end', function()
    window.moveTo(x - (window.window.width / 2) - 6, y);
    window.show();
    window.focus();
  });
}
// show panel when click in tray
tray.on('click', function (evt) {
  showPopup(evt.x, evt.y);
});