Even though I'm sort of a broken clock with this one, Java XML API uses Factory a lot. I mean just look at this:
Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(source);
String title = XPathFactory.newInstance().newXPath().evaluate("//title", doc);
...and so on and so forth.
Additionally various Buffers (StringBuffer, ByteBuffer, StringBuilder) use Builder.