1) src -- Contains the source code (.java files)Why?
2) build -- contains .class filesNo. The .class files have to be in the JAR file according to their packages. You can't change that. No 'build' directory.
3) images -- contains necessary imagesSure.
4) sounds -- contains necessary sounds
Also, the executable JAR should install JMF (the JMF exe should also be a part of this JAR file, I guess) and set the CLASSPATH to the JAR files associated with JMF...No. JAR files can't 'install' things. You should distribute JMF along with your JAR file, to be installed in the same place, and name it in the Class-Path entry of your JAR file's manifest.mf. Unless the JMF jar needs to be installed in jre/lib/ext, in which case you will just have to arrange for that to happen - no JAR file can do that for you.