If you
are developing a web application you can do so using a lot of libraries
and technologies. The first and the foremost criteria is the features
that you need for your web application. Based on your requirement you
can choose the technology and the model in which you want to develop
your web application.
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You
could use a native XML database like eXist if you need work extensively
with XML database. There are libraries meant for manipulating the XML
documents like DOM, JAXP, and JAXB.
Libraries
like dom4j and JDOM can also be used for working with your XML documents.
With these libraries you can create an XML file, edit an XML file and
manipulate them and transform them in other forms.
If serializing
the java classes to XML is needed you can go for library like XStream.
A simple search on the internet would provide you link to all these
libraries and the best of them is that all are open source. So there
is nothing wrong in trying these libraries for your web application
and many developers are using them.