VisualVM is a visual tool integrating several commandline JDK tools and lightweight profiling capabilities. Designed for both production and development time use, it further enhances the capability of monitoring and performance analysis for the Java SE platform.
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.