<run xmloutputversion="1.02">
    <info type="a" />
    <debugging level="0" />
    <host starttime="1237144741" endtime="1237144751">
        <status state="up" reason="somereason"/>
        <something avalue="test" test="alpha" />
        <target>
            <system name="computer" />
        </target>
        <results>
            <result id="1">
                <state value="test" />
                <service value="gamma" />
            </result>
            <result id="2">
                <state value="test4" />
                <service value="gamma4" />
            </result>
        </results>
        <times something="0" />
    </host>
    <runstats>
        <finished time="1237144751" timestr="Sun Mar 15 19:19:11 2009"/>
        <result total="0" />
    </runstats>
</run>

<run xmloutputversion="1.02">
    <info type="b" />
    <debugging level="0" />
    <host starttime="1237144741" endtime="1237144751">
        <status state="down" reason="somereason"/>
        <something avalue="test" test="alpha" />
        <target>
            <system name="computer" />
        </target>
        <results>
            <result id="3">
                <state value="testagain" />
                <service value="gamma2" />
            </result>
            <result id="4">
                <state value="testagain4" />
                <service value="gamma4" />
            </result>
        </results>
        <times something="0" />
    </host>
    <runstats>
        <finished time="1237144751" timestr="Sun Mar 15 19:19:11 2009"/>
        <result total="0" />
    </runstats>
</run>

<run xmloutputversion="1.02">
    <info type="a" />
    <debugging level="0" />
    <host starttime="1237144741" endtime="1237144751">
        <status state="down" reason="somereason"/>
        <status state="up" reason="somereason"/>
        <something avalue="test" test="alpha" />
        <target>
            <system name="computer" />
        </target>
        <results>
            <result id="1">
                <state value="test" />
                <service value="gamma" />
            </result>
            <result id="2">
                <state value="test4" />
                <service value="gamma4" />
            </result>
    	    <result id="3">
                <state value="testagain" />
                <service value="gamma2" />
            </result>
            <result id="4">
                <state value="testagain4" />
                <service value="gamma4" />
            </result>
        </results>
        <times something="0" />
    </host>
    <runstats>
        <finished time="1237144751" timestr="Sun Mar 15 19:19:11 2009"/>
        <result total="0" />
    </runstats>
</run>

public class MergeXmlDemo {

  public static void main(String[] args) throws Exception {
    // proper error/exception handling omitted for brevity
    File file1 = new File("merge1.xml");
    File file2 = new File("merge2.xml");
    Document doc = merge("/run/host/results", file1, file2);
    print(doc);
  }

  private static Document merge(String expression,
      File... files) throws Exception {
    XPathFactory xPathFactory = XPathFactory.newInstance();
    XPath xpath = xPathFactory.newXPath();
    XPathExpression compiledExpression = xpath
        .compile(expression);
    return merge(compiledExpression, files);
  }

  private static Document merge(XPathExpression expression,
      File... files) throws Exception {
    DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory
        .newInstance();
    docBuilderFactory
        .setIgnoringElementContentWhitespace(true);
    DocumentBuilder docBuilder = docBuilderFactory
        .newDocumentBuilder();
    Document base = docBuilder.parse(files[0]);

    Node results = (Node) expression.evaluate(base,
        XPathConstants.NODE);
    if (results == null) {
      throw new IOException(files[0]
          + ": expression does not evaluate to node");
    }

    for (int i = 1; i < files.length; i++) {
      Document merge = docBuilder.parse(files[i]);
      Node nextResults = (Node) expression.evaluate(merge,
          XPathConstants.NODE);
      while (nextResults.hasChildNodes()) {
        Node kid = nextResults.getFirstChild();
        nextResults.removeChild(kid);
        kid = base.importNode(kid, true);
        results.appendChild(kid);
      }
    }

    return base;
  }

  private static void print(Document doc) throws Exception {
    TransformerFactory transformerFactory = TransformerFactory
        .newInstance();
    Transformer transformer = transformerFactory
        .newTransformer();
    DOMSource source = new DOMSource(doc);
    Result result = new StreamResult(System.out);
    transformer.transform(source, result);
  }

}

Doc A:
<root>
  <a/>
  <b>
    <c/>
  </b>
</root>

Doc B:
<root>
  <d/>
</root>

Merged Result:
<root>
  <a/>
  <b>
    <c/>
  </b>
  <d/>
</root>

XPath.resultsNode=results
action.resultsNode=MERGE

<xsl:param name="mDocName">yoursecondfile.xml</xsl:param>
<xsl:variable name="mDoc" select="document($mDocName)" />

<!-- Copy everything including attributes as default action -->
<xsl:template match="*">
    <xsl:element name="{name()}">
         <xsl:apply-templates select="@*" />
        <xsl:apply-templates />
    </xsl:element>
</xsl:template>

<xsl:template match="@*">
    <xsl:attribute name="{name()}"><xsl:value-of select="." /></xsl:attribute>
</xsl:template>

<xsl:template match="events">
    <xsl:variable name="allEvents" select="descendant::*" />
    <events>
        <!-- copies all events from the first file -->
        <xsl:apply-templates />
        <!-- Merge the new events in. You need to adjust the select clause -->
        <xsl:for-each select="$mDoc/logbook/server/events/event">
            <xsl:variable name="curID" select="@id" />
            <xsl:if test="not ($allEvents[@id=$curID]/@id = $curID)">
                <xsl:element name="event">
                    <xsl:apply-templates select="@*" />
                    <xsl:apply-templates />
                </xsl:element>
            </xsl:if>
        </xsl:for-each>
    </properties>
</xsl:template>

<xsl:template match="logs">
     <xsl:element name="logs">
          <xsl:apply-templates select="@*" />
          <xsl:apply-templates />
          <xsl:apply-templates select="$mDoc/logbook/server/logs/log" />
    </xsl:element>