This page describes a number of steps which should be taken to ensure that security best practices are followed and enforced.
The 1.5.x series of releases of WSS4J is deprecated. You should switch to a 1.6.x release as a matter of priority, as this branch contains up to date security fixes. For example, WSS4J 1.6.x uses the "secure validation" mode of Apache XML Security for Java, which protects against a number of attacks on XML Signature.
You should always upgrade to the latest minor release in a timely manner, in order to pick up security fixes.
WSS4J can be used with a web services stack such as Apache CXF or Apache Axis in one of two ways: either by specifying security actions directly, or via WS-SecurityPolicy. WS-SecurityPolicy is a much richer way of specifying security constraints when processing messages, and gives you more "automatic" protection against various attacks then when configuring via security actions. See for example, this blog post on XML signature wrapping attacks. Therefore, you should always try to use WSS4J with a WS-SecurityPolicy requirement.
WSS4J supports two key transport algorithms, RSA v1.5 and RSA-OAEP. A number of attacks exist on RSA v1.5. Therefore, you should always use RSA-OAEP as the key transport algorithm, and enforce this decision. For WS-SecurityPolicy, this means to avoid using any AlgorithmSuite that ends with "Rsa15" (e.g. "Basic128Rsa15"). For the direct configuration case, you should explicitly configure WSHandlerConstants.ENC_KEY_TRANSPORT ("encryptionKeyTransportAlgorithm") to be "http://www.w3.org/2001/04/xmlenc#rsa-oaep-mgf1p". This latter point requires the web services stack to set this property on the Request (it is known that Apache CXF does this).
There are some attacks that exploit the "cbc" mode of a Symmetric Encryption Algorithm. WSS4J has support for "gcm" mode algorithms as well. This can be specified via WSHandlerConstants.ENC_SYM_ALGO ("encryptionSymAlgorithm"), for example to "http://www.w3.org/2009/xmlenc11#aes128-gcm".
WSS4J 1.6.7 introduced the ability to specify regular expressions on the Subject DN of a certificate used for signature validation. It is important to add this constraint when you are supporting "chain trust", which is where you are establishing trust in a certificate based on the fact that the Issuer of the certificate is in your trust store. Otherwise, any certificate of this issuer will pass trust validation. See here for more information.
When not using WS-SecurityPolicy (see point above about favouring the WS-SecurityPolicy approach), you should specify a signature algorithm to use on the receiving side. This can be done via WSHandlerConstants.SIG_ALGO ("signatureAlgorithm"). Setting this property to (e.g.) "http://www.w3.org/2000/09/xmldsig#rsa-sha1" will ensure that the signature algorithm allowed is RSA-SHA1 and not (e.g.) HMAC-SHA1. This latter point requires the web services stack to set this property on the Request (it is known that Apache CXF does this). See also the previous point about setting the key encryption transport algorithm.