Java Applet and JavaScript has some different options and handles zooming and scaling differently.
Java Script is more lightweight for the viewing browser. Java applet requires that the viewers have java installed on their computer.
Try both and see what you prefer. I prefer JavaScript
One reason I asked is because I was using javascript with the latest Beta, with a Logitech 9000 at 720 and it works fine with the latest Firefox, but with IE8 (on two entirely different PCs), the image would flash white in between frames, which makes for unpleasant viewing.