Not having used Javadoc or pod 'in anger' yet (I am but a university student and students only doc their code if they get marks for it), I can say that the plain old mark-up system of pod looks very easy to use. Javadoc, on the other hand, makes much prettier documentation, but has a more difficult syntax and you need an html viewer to look at it. The Javadoc convention of putting the documentation above a method and explaining all your params and return values is good.
I have a wiry brain/each eye a camera. Robot Tourist, by Ten Benson