As the title asks, and:

what is the main reason why I don't see a whole lot of Java apps online?

Since the GPL'ing of Java, will we see more Java Apps replacing Flash?

Any other comments on Java?

-- BTW --

JavaScript and Styles for games and eye candy slows down the page. Java should make a difference in speed right?

The main reason is Java is far more used on the server side nowadays.
Possibly. One other reason that may happen would be Java performance being now much better than it used to be.
Not particularly, Javascript is already fast.

Well, since you asked, my -- Java became useful with the introduction of generics; since Java 5 we've finally been able to write Java code that's almost as powerful as C++. Now Java 6 has a really nice performance boost, at least on my systems, and I'm very pleased to see it being offered in the Ubuntu Feisty Fawn repositories. It's a nice generic language for nice generic people solving nice generic problems; unless you're a Java Guru, in which case you can do basically anything you want with reflection. Too damn many libraries means you can basically write an entire application using everybody else's code -- that's a good thing. Anyways...

While I've never had too any bad problems with JavaScript slowing down a page, I would think that you'd basically be trading speed at load time for speed at runtime. You know, kind of like the compiled vs. interpreted debate -- where do you want to lose performance at?

While I have a certain disdane for Java, I would much rather see a java coded page than a flash page, not only for size but also in some cases speed. Although the JVM is initially designed to run on any platform without recompiling, that is also the main reason for it's slowness however compared to flash nowadays, it is no where near the resource hog that flash is.

Now in your next question about Java being GPL'ed, there are still certain Java libraries perhaps that will have to be written again from scratch only because certain parties have written them that are their own and not from Sun, therefore Java being released under the GPL won't exactly cover 100% of Java.

Actually the "Flash Player" is also a virtual machine designed to run on many platforms without recompiling.
Nothing really different than the JVM, but well marketed: A "Player" is something less scary to install than a "Virtual Machine" for a casual user.