put jar in the endorsed folder
put the wsdl4j-1.6.1.jar in the $WebSphere_HOME/java/jre/lib/endorsed folder.
In the WebSphere console, find the specific enterprise application, click the "Class loading and update detection".
Mark the "Classes loaded with application class loader first" selected.
Mark the "Class loader for each war file in application" selected.
And then restart the Websphere server. (Because we changed the endorsed folder, we need to restart it to make it take effect).
Please make sure your classpath doesn't have the servlet-2.5 library, since WebSphere6.1 is servlet-2.4 compliant!
Add your own class loader
If you put your wsdl4j-1.6.1 jar in $WAS_HOME/java/jre/lib/endorsed, all your applications 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.
Step by step
In the WAS console navigate to Environment > Shared Libraries
Select the scope you wish your library should be visible in
Click New and set values ex: name=MYAPP_SHARED_LIB, classpath=PATH_TO/wsdl4j-1.6.1.jar and Save
Navigate to Application servers > [your server name] > Java and Process Management > Class loader > New
Select Classes loaded with application class loader first and Save
Select your new class loader and click Shared library references
Add your shared library (MYAPP_SHARED_LIB) Save and restart your server.
Tested in WAS 6.1 only but should work in earlier versions as well.