First, do you know any Java? Regardless of what you want to do with Java, you need to learn the fundamentals first. The best way to do this is with a good introductory book, like Head First Java. In the meantime, you might try The Java Tutorial online.
Second, what exactly do you want this web-based application to do? Do you know whether you want this to be an applet? Or are you thinking about Servlets/JSP?
"We're kind of on the level of crossword puzzle writers... And no one ever goes to them and gives them an award." ~Joe Strummer sscce.org