xerces is jaxp compliant, as are most of the best (most widely used) parsers. jaxp compliance just assures you a 'known' parser interface ... what happens next is a matter of the specific parser implementation. for example, you can't guess what parser features a given parser implements - features vary widely across parsers.
to un-cart the proverbial horse ... as i understand it:
. jdom (since 2003) integrates jaxen for xpath support. jaxen requires jaxp.
. jaxp has been bundled into sun's
java class lib since 1.4
...so you'll get jaxp under either scenario and the question becomes which parser impl best satisfies your specific requirements.
i, like Lasse, prefer Xerces for the reasons he stated. however, it seems more of a religious question among practitioners these days... you can pretty easily do some performance tests using representative documents. jaxp makes it simple for you to run comparison tests with various parsers:
hth