In Java SE, Swing and AWT there is a method setAlwaysOnTop(boolean) to set a JFrame or Frame on top of all windows in a JavaSE desktop application. But JavaFX right from its first release was lacking such a method.
So after a long wait, it looks like the Developers wish is about to come a true through the resolution of JIRA RT-153 [https://javafx-jira.kenai.com/browse/RT-153] which now shows fixed and the fix will be available in JDK 8u6 or 8u20 which is said to be released in the second half of 2014. So the Stage will have a method to make it on top of the rest.
UPDATE: Early access now available for JDK 8u20(here) also a short article on alwaysontop by carl : http://java.dzone.com/articles/javafx-8u20-days-future-past