RT-997 provided the ability to get FPS data from any FX app by setting up a standard logging.properties file. Output is similar to the following:
...
Jun 16, 2009 5:03:17 PM com.sun.scenario.scenegraph.Logger$UtilLogger log
INFO: 71.07 FPS
Jun 16, 2009 5:03:20 PM com.sun.scenario.scenegraph.Logger$UtilLogger log
INFO: 71.10 FPS
...

As of Marina b11, the output now looks like:
...
Jun 16, 2009 5:11:50 PM com.sun.scenario.scenegraph.JSGPanel$FPSData nextFrame
FINE: %.2f FPS
Jun 16, 2009 5:11:53 PM com.sun.scenario.scenegraph.JSGPanel$FPSData nextFrame
FINE: %.2f FPS
...