We developed several web applications for different customers, from simple kind-of-boring-looking CRUD-style GUIs for those poor admin guys to fancy-schmancy AJAX-enhanced GUIs
I'd go for HTML 5, unless I had some needs a web app couldn't satisfy.
I'm certain you can build great apps with JavaFX, but there is very little tooling, except for the standard Java stuff. And since it's not very widely used, you'll have trouble finding support, and hiring people who are good at it. There's also always the risk of it going the same way as its .Net counterpart Silverlight - to the trash can (Oracle aren't sentimental). As for Flex, Adobe just donated Flex to Apache with the explanation that HTML 5 is the "best technology for enterprise application development".
Compare this with HTML 5. It's not only more widely used (which means you'll be able to find support and have an easier time recruiting), but it also gains more support, better tooling and new features continually. I think it's rather obvious which is more future proof.