In a previous posting I talked about connecting jConsole to connect Tomcat and JBoss, this time I will discuss WebSphere.  The short version is that this is not as simple as Tomcat or JBoss because connecting to the running process will not work.  If you just need MBean information I would suggest sticking with BeanSpy to get the information you want.  However, if there is something that you normal want to see in jConsole, below is some links that will be useful.

WebSphere 6.1

Resource: stackoverflow

The short version is that this really is not possible without re-writing your code.  IBM provides a developer tool called RAD (Rational Application Developer - non-free tool with 60 day eval).  If you run your application in there you can connect jConsole to this, depending on your time requirements and what exactly you want to do, it might be easier to stick with using BeanSpy.

WebSphere 7.0

With version 7.0 it is possible to connect jConsole to WebSphere. Below are two postings that I found helpful in doing this. 

Resources: