But remember Java and JavaScript are two DIFFERENT things. You'll want to stay away from javascript in general too, as it is not very accessible (although there are many exceptions to this rule).
But to answer your question, IMHO a GOOD website has clean, structured code (Try to aim for atleast XHTML 1.0 Tansitional), is usable (go read the books "Designing Web Usability" by Jakob Nielson, and "Don't make me think" by Steve Krug), accessible (read
http://www.joeclark.org/book/sashay/serialization/ ) has a clean look (browse the sites around
http://cssvault.com) and presents itself in a proffesional way.
But, that's just my opinion. Whatever.