Here is how I would do it:
There may be further subdivion under this if you want.
> Or should I make subtree:
> src/main/ejb and org.xxxx.yyy for all ejb's and
> src/main/jmx and org.xxxx.yyy for all mbeans
> and modify build.xml?
Yep, that's how i would do it. You'll different jars for deployment anyway. Of course you could generate different jars from one source tree (e.g. src/main/org/xxx...) also, but personally i think that is bad practice and leads to less understandle and maintainable source code structure and build files.