We did a bit of research on how we could monitor WebSphere Application Server and created a patch against trunk, r39265, that allows us to monitor some of the items on the default installation of WAS.
File websphere.patch does several things. First of all, it modifies the currently hardcoded JMX service URL to that of WAS. Then, it changes one of the catch clauses to protect against NoClassDefFoundError, which we otherwise do not catch or log. Finally, it adds WAS JAR files to CLASSPATH in startup.sh and sets Java options for a secure connection to WAS, similar to http://blog.monitis.com/index.php/2012/09/12/configuring-jmx-in-websphere-8-5/ .
Using the patch we were able to monitor some WAS-specific items. In order to see what items can be monitored, you can use the undocumented jmx.discovery item. It works in the same way that net.if.discovery and vfs.fs.discovery work, except it is of type "JMX agent". The reason it is undocumented is because it returns a list of JMX counters of various types, but our low-level discovery currently does not have a facility to create items whose type is not known in advance, which makes it not very useful.
Anyway, jmx.discovery can be used to explore your Java application for supported JMX counters by attaching an item prototype, similar to that in item-prototype.png, to the discovery rule. All created items will have type of "Character", which is not very useful, but it will give a nice list of supported items you can monitor and create interesting ones manually.
We like the idea of being able to specify JMX service URL on the host's interface level, as proposed in this feature request, and this is currently the approach we are considering for development. However, it requires significant effort and considering that our current focus is getting Zabbix 2.2 ready for release, we cannot do this at the moment.
In the meantime, if you could use the idea from websphere.patch, apply it to your installations (not only WAS, but other software, too) and share your experience, it would be great and might help us to do the full implementation.