Alfred,
We chose to package most of the samples using Web Start, because in our experience it has the best deployment experience for users regardless of their browser or OS configuration. However, any of the samples can be run via Web Start or as Applets simply by toggling the deployment settings in the supplied Netbeans project and rebuilding.
As an aside, the Mobile examples in Chapter 10 are actually deployed as applets, so if you want to see a JavaFX example running as an applet you can go here:
http://jfxtras.org/portal/pro-javafx-platform?p_r_p_564233524_tag=chapter+10