Stephan Becker posted advice on debugging problems with Adobe Experience Manager. He explains how to use quite a few. Thread Dump Analyzer is great.
One thing that I like to use is a heap dump, which he doesn’t mention. Heap dumps have the disadvantage of being extremely large. Their advantages come when trying to find the ultimate culprit of bad behavior, especially memory-related problems.
NetCentric: Analysing Issues Properly in AEM