Improve documentation for WebSphere setup: http://cwiki.apache.org/CXF20DOC/appserverguide.html#AppServerGuide-Websphere
If you put your wsdl4j-1.6.1 jar in $WAS_HOME/java/jre/lib/endorsed as suggested in the wiki all your application will depend on your version of wsdl4j. Another solution is to create a new class loader in your server which loads before parent class loader, create a shared library with your version of wsdl4j and add this shared library to your new class loader. This version of wsdl4j will only be available for your specific server and not affect applications running in other servers.
Tested in WAS 6.1 only but should work in earlier versions as well.
Step by step
1. In the WAS console navigate to "Environment > Shared Libraries"
2. Select the scope you wish your library should be visible in
3. Click "New" and set values ex.: name=MYAPP_SHARED_LIB, classpath=PATH_TO/wsdl4j-1.6.1.jar and "Save"
4. Navigate to "Application servers > [your server name] > Java and Process Management > Class loader > New"
5. Select "Classes loaded with application class loader first" and "Save"
6. Select your new class loader and click " Shared library references"
7. Add your shared library (MYAPP_SHARED_LIB) save and restart your server.
This should do it.