Oxygen XML Diff is a complete solution for comparing and merging XML files. It offers both directory and file comparison, six different diff algorithms, and multiple levels of comparison. The comparison can also be performed inside ZIP-based archives (ZIP, JAR, ODF, OOXML). Oxygen XML Diff includes two specialized XML-aware comparison algorithms: XML Accurate, tuned for precise comparison, and XML Fast, tuned for speed at the expense of some accuracy.
JDiff is a tool which performs folder recursive comparisons and file comparison based on Myer's minimum set of differences algorithm. Based on this file comparison algorithm, it also provides a 3-way merge, which can run without a graphical interface. JDiff is released as an auto-executable jar file.