Here's bunch of other XML difference tools:

• IBM AlphaWorks XML Diff and Merge Tool - Java based, uses tree matching based on ID attributes or content
• Dommitt Unordered Diff - ignores order of nodes in document (?!), Java based, flattens DOM trees to arrays then does step by step comparison to generate insert, delete, update and nochange operations.
• diffxml - GPL, Java based, algorithm detailed in author's dissertation [postscript]
• XML::SemanticDiff - Perl module, artistic license, event driven parser, seems to handle namespace changes
• DeltaXML - commercial application, Java based, tree matching, root elements must be the same

Some other pointers that might be relevant: XUpdate [xmldb] (appears dead), X-Diff Algorithm [citeseer], Algorithm::Diff perl module.