assertEquals(query1,query2)
this works *most of the time*. it's currently a very rudimentary comparison: it just converts each query to a string (like json) and then compares the strings.
to see the differences, you can use the "compare tool" in the plugin. To see what this looks like, run "mxunit.PluginDemoTests.CompareDialogTest" in the MXUnit view in Eclipse. Then, highlight the queryCompareDifferences test and click the little 'book'-looking button in the middle part of the view. It'll pop up a compare dialog and you can use the "next change" and "previous change" buttons on the far right to navigate through the differences.