I don't think either are directly related, so to speak. Meaning whether HTML 3, 4, or 5 I still might need some backend serverside functionality and Java might be that language. But they still are related in the sense of if you have server side functionality, which language do you want to use. Some web apps might be perfect to go back to a client-server like approach where the HTML is accessing the DB directly. Heck HTML5 has a small database locally on the client side.
However, as I build my website I am asking myself more and more about what language/serverside or serverside at all to use. I am having real problems/issues with the JSP/Servlet Spec and what you have to do to get things to work how you want them, even with Frameworks built on top of JSP/Servlet spec. Which is why I am very interested in the Play Framework - Java without the JSP/Servlet spec and not JSP/Servlet Container. But then there are other frameworks like Grails that get rid of lots of the JSP/Servlet spec that I despise. Grails is built on top of JSP/SpringMVC but removes so much of the pain points from you handling it yourself.
But then I start to question on whether I should go down the PHP or RoR(Although I have the same dislike for RoR), or Python. Who knows.
But I don't think my decision, on any of this has to do with the version of HTML that I am using.
Fair enough. I guess where I'm coming from is the range of features offered in HTML5, which will facilitate client side functionality and accelerate the march towards the rich user interfaces of thick clients. In this scenario, I was thinking that a new paradigm for web programming may evolve leaving Java as a language of yesteryear.