The soon-to-be released WSS4J 1.6 has been ported to use the JSR 105 API for XML Digital Signature. Previously, WSS4J 1.5.x used the custom API of the Apache Santuario XML Security for Java library to create and process XML Digital Signatures.
WSS4J 1.6 has a minimum requirement of JDK 1.5 (note that WSS4J 1.5.x supports JDK 1.4). As JDK 1.5 does not contain an implementation of JSR 105, this means that XML Digital Signature is done via the JSR 105 implementation of Apache Santuario. However, when JDK 1.6+ is used, WSS4J 1.6 uses the JDK implementation of JSR 105 for signature creation and verification. You can override this by endorsing the Santuario jar.
The Apache Santuario XML Security jar is still required for the JDK 1.6 case, as there are compile-time dependencies in WSS4J for encryption/decryption, as well as for some algorithm parsing, and resource resolver stuff. One downside to the Santuario jar, is its dependence on Xalan for a small subset of operations. This dependency will be removed for the 1.5 release of that library (in a few months).
It is worth noting some changes to the main class used in WSS4J for signature creation as a result of the JSR-105 port. In WSS4J 1.5.x, after the signature certs and list of references to sign had been configured, the "computeSignature" method was called to compute the signature. The DOM element corresponding to the signature was independent of the pre-existing security header, and could be extracted later and inserted into the security header.
In WSS4J 1.6, you must tell "computeSignature" where to insert the signature element. A boolean "prepend" argument allows you to configure whether to prepend the generated Signature element to the security header, or whether to append it. If prepend is true, then an optional siblingElement argument can be used to prepend the signature element before this sibling element. Once computeSignature has been called, you have no control over where the signature element is inserted into the security header.