JMeasurement is a free and simple java api for monitoring runtime and usage (count, parallel activation, last activation) of user defined points in java production code. It is simple to use and extended. JMX is supported.
Stopwatch was ment to replace System.currentTimeMillis() calls, match like Log4j replaced System.out.println() calls. To see how it does that go to Quick Start page.
InfraRED is a tool for monitoring performance of a J2EE application and diagnosing performance problems. It collects metrics about various aspects of an application's performance and makes it available for quantitative analysis of the application.