Choose XML if you need to interoperate with systems you don't control (XML Schema is invaluable here), if you will be transforming the data extensively into text, HTML, or XML (haters notwithstanding, XSLT is peerless), if your data includes a lot of text markup, if your data needs to be human-editable (haters notwithstanding, editable XML that's validated against a schema is a pretty good tool for a lot of jobs), and/or if you need to interoperate any of the myriad of tools and technologies that work with XML.
Choose JSON if you really can't be bothered with any of the above.
Choose YAML if you're working in an environment that's got a lot of YAML support.
