Three common problems related to the java application performance can be categorized into three types:

• High CPU Contention
• Deadlock
• Memory Leak

Sometimes its really really hard to find the object that causing those problem, but with nowadays feature for heap profiling since jdk1.4 help us to identify our root problem.

usually we can run those feature using -XX option, for example:

java -Xms32m -Xmx64m -Xrunhprof:heap=dump,monitor=y,cpu=samples,thread=y,file=<dir>

with those option we can snapshot statistic of the JVM behavior and analyze the result with your favorite tools. Based on my experience of troubleshoot the application usually i use two tools IBM HeapAnalyzer (tool to identify the memory leak problem), and PerfAnal (tool that provide an analysis of CPU contention problem).

I think it become more and more obvious, that developing application with Java will give you a full control of the application itself.