What is usually not mentioned is the fact that when you specify a non-standard target directory, it must not contain any spaces. The easiest way to achieve this is the use of the 8.3 format. So instead of “C:\Program Files” you can use “C:\Progra~1”.
One of the less known libraries of the Apache Commons project is JXPath which implements XPath (and not only for accessing Java beans but of course also DOM structures). Documentation, however, is scarce so the tutorial provided on http://www.tfo-eservices.eu/wb_tutorials/media/JXPathTutorial/PDF/JXpathTutorial.pdf is something you want to look at.
I recently looked into the subject of cross-platform installation. In this context I have come across the multi-platform installer IzPack (there is also an interview on InfoQ). Although this creates Java installers, as opposed to native formats like MSI or RPM which I prefer, it seems to be an interesting product. So I will spend some more time with it and keep you posted on my findings
Nicolas Whitehead has written a very nice series of articles on Java run-time monitoring. They are published at the IBM Developer Works site and you should definitely check them out.