The three most popular tools for monitoring web servers and WAS that I see in the field are IBM Tivoli Composite Application Monitor family, Wiley, and Dynatrace. Note these are used for primarily monitoring middleware only.
You can also use the Tivoli Performance Viewer that cames with WAS for monitoring.
WAS and the WebSphere plugin also support the Application Response Measurement v4 spec (output can be sent to the WAS log file system or another ARM enabled monitoring tool).
You can also write your own monitoring tools that access JMX interface.