I don't doubt the claim that a Java Applet can be faster than JavaScript, but I haven't ever seen a modern high-performance web application written as a Java Applet. The CAD stuff, games, etc., are always Flash (EDIT: when they aren't JavaScript). So the comparison is really Flash vs. JavaScript.
And… comparing Flash to V8? I'm having trouble finding modern benchmarks, but Flash is based on ActionScript, which is related to JavaScript. JavaScript has V8, which is a world-class JIT with Google's engineering talent behind it. I'd be very surprised if Flash's JIT was competitive with V8. At least as of 2011 it wasn't [1].