There is a difference between web design and web development. The most popular language for web design is html using CSS (cascading style sheets). This allows the designer to separate the content from the style formatting and control it more easily.
CSS can also be used to do many things that some developers use Flash and Java for, drop down menus for example. The trouble with Flash and Java is that they are not search engine friendly i.e. search engines can't decipher the code to see what it means and consequently ignores it.
Web development does typically refer to the generation of scripts to add functionality to a site that isn't always available through html and css. One of the most popular for server side includes is, as stated by Vladi, php. But Java must also be pretty close and Flash for dynamic graphics etc.