Java is not the same as Javascript.. Javascript is enabled in >90% of browsers I would expect maybe >95%, normally only security concerns cause people to turn it off.
Javascript is probably the way to go as it can then be crawled by GoogleBot (aslong as all links are present in the markup when the page loads). Now, many years later, Google cannot crawl flash very well or even at all in most cases.
Stick with HTML where possible.
