More importantly, Phylets allow you to go beyond the typical Java simulation by creating applications that require active participation from the student. Students can be asked to analyze motion using parameters that must be inferred from "measurements" taken from the computer screen.
The authors have recently published a book that provides a wealth of tutorial and pedagogical information.
A Physlet only does what your scripts tell it to do. Therefore the usability and effectiveness a particular Physlet application has much more to do with the associated scripts than with any particular Physlet.
Getting started with your first Physlet application can be a bit daunting. The very best approach is to copy the source (just right-click on the browser screen) from an application you want to use. You can download the java archives (jar files) if you want to host the application on your server.
Most folks with just a bit of programming background will find it easy to modify existing scripts to produce customized applications. The Physlet book and the Physlet website have tons of example script to start with.