There are various tools that I use to spot issues and investigate an enterprise environment.
One of my favourite tools is IBM Performance Analysis Suite.
Capabilities described by IBM:
Import all kinds of performance data for analysis. Some examples: DB2 snapshot, Java verbose GC output, Java thread dumps.
Import software/middle-ware configuration for compliance checking. Some examples: configuration of DB2, Oracle, WebSphere, and operating systems.
Provide a rule engine for defining alerts to detect symptoms from the imported data. An out-of-box pre-defined set of rules are provided, based on common performance best practice of supported software and middle-ware.
For example the following is a nice tutorial on how to use it to analyse DB2 Snapshots Using IBM Performance Analyst to Analyze DB2 Snapshots
One of the greatest features is in fact the menu of the tool. In the File-Open dialog you get in fact tutorials on how to generate the investigation/trace data.
The other tool I use is the VisualVM. This is a tool that can analyse the java core dumps but can be linked to running instances of JVM for monitoring.