If I have an application written in Java, how can I make it available for purchase/download on my website? Namely, how do I obscure the source code so it can't be viewed, yet enable it to be executed by any machine (including ones that don't have the JVM installed)?

you can make it an exe file using java launcher then using Paypal you can upload it and make it available for purchase or download. Or you can upload it to a site like Megaupload and make some cash while distributing your game for free.