Hi, I think php is the way to go for server side stuff.
Check out dhtml for effective use of java or object oriented stuff. You can find alot of menus for instance that are dhtml and fully accessable(wcag).
Java script is not so much a problem as long as you call the .js file instead of sticking it in the markup.
You can start here
DHTML Tutorial
or google dhtml and you will find loads of stuff.
hope that helps
Nigel