Icons

Title bar icon

To change icon in title bar of your app, put a reference to PNG/JPG into package.json

{
  ... other stuff here ...
  "window": {
     "icon": "path/to/my/app.png"
  }
}

Application icon

This is platform specific unfortunately.

Windows

After creating package you would have to use resource editor to change bundled icon. Some sources recommend freeware Resource Hacker which would do the trick ( example )

OSX

Assuming you have your icon in PNG/JPG format, you'd first need to convert it to icns file format. There are different ways to accomplish this, but the easiest is probably using free version of IMG2ICNS. Drag your image into app window and export resulting icon as nw.icns. You'd need to replace default nw.icns inside Your.app/Contents/Resources. Or you may want to change the name of your icon to something like mysupericon.icns and change the value of CFBundleTypeIconFile in Your.app/Contents/Info.plist to reflect new name. Additionally, you'll also need to take the Icon file (generated by the "Folder" option in Img2icns) and place it inside the root of the app's Package Contents.

Check out this thread on other simple ways to create icns files

Linux

You'd need to create proper .desktop file.