Hi there,
I wrote a small test program where I use the FPSAnimator and call setAlwaysOnTop() in the init() method:
https://github.com/codeanticode/jogl2-tests/blob/master/src/test/windows/WindowTopNEWT.javaIt works as expected on Windows (10) and Linux (Ubuntu 12.04 with default window manager), but it does not on Mac OSX (10.9.5). I can file a bug report if needed.
Andres