Yammer Metrics

http://www.javacodegeeks.com/2012/12/yammer-metrics-a-new-way-to-monitor-your-application.html
http://metrics.codahale.com/getting-started/
http://metrics.codahale.com/manual/core/#man-core-reporters-slf4j
http://metrics.codahale.com/manual/servlets/#manual-servlets
JConsole, System Console, Ganglia, Graphite, CSV, or making them available through a web server.
Timers.

Very advanced, does monitoring and other enterprise features.

Perf4j
http://perf4j.codehaus.org/
just for timing metrics
http://perf4j.codehaus.org/devguide.html
http://www.infoq.com/articles/perf4j
now on github
Parse log files with tool for stats report, csv, google charts
log4j or logback required
can use annotations, direct call or aspects
work restarted recently
maven: http://repository.codehaus.org/org/perf4j/perf4j/
http://mvnrepository.com/artifact/org.perf4j/perf4j

JavaSimon
https://code.google.com/p/javasimon/
https://code.google.com/p/javasimon/wiki/MavenSupport
https://code.google.com/p/javasimon/wiki/JavaEE
https://code.google.com/p/javasimon/wiki/Readme
Microbenchmarks:
https://code.google.com/p/javasimon/wiki/Microbenchmarks
Simple to use
https://code.google.com/p/javasimon/wiki/GettingStarted
https://code.google.com/p/javasimon/wiki/PerformanceResources
includes a webconsole: https://code.google.com/p/javasimon/wiki/WebConsole
https://code.google.com/p/javasimon/wiki/WebConsolePlugins
https://code.google.com/p/javasimon/wiki/Introduction
Performance measurement plus timers
monitoring
improvement over http://jamonapi.sourceforge.net/

Timing Issues
http://www.ibm.com/developerworks/java/library/j-benchmark1/index.html#table1
https://www.ibm.com/developerworks/java/library/j-benchmark2/
http://www.ellipticgroup.com/html/benchmarkingArticle.html
https://code.google.com/p/caliper/wiki/JavaMicrobenchmarks
http://www.ibm.com/developerworks/java/library/j-jtp02225/

Microbenchmarking

Caliper
https://code.google.com/p/caliper/
https://code.google.com/p/caliper/wiki/BestPractices

jmh
http://openjdk.java.net/projects/code-tools/jmh/
http://webcache.googleusercontent.com/search?q=cache:V1ij-eU-QvEJ:psy-lob-saw.blogspot.com/2013/04/writing-java-micro-benchmarks-with-jmh.html+&cd=4&hl=en&ct=clnk&gl=us
http://shipilev.net/pub/talks/jvmls-July2013-benchmarking.pdf

JAPEX
https://japex.java.net/
https://japex.java.net/docs/manual.html

Monitoring

Java Melody
https://code.google.com/p/javamelody/
https://code.google.com/p/javamelody/wiki/Screenshots#Charts
JIRA plugin, jar for web integration, Confluence plugin
https://marketplace.atlassian.com/plugins/net.bull.javamelody
used by Jenkins
https://wiki.jenkins-ci.org/display/JENKINS/Monitoring
Example Site: http://demo.javamelody.cloudbees.net/monitoring

Servo
http://webcache.googleusercontent.com/search?q=cache:Y3mMIVEAVsMJ:https://github.com/Netflix/servo/wiki+&cd=1&hl=en&ct=clnk&gl=us

btrace with visualjvm for local
https://kenai.com/projects/btrace

Java run-time monitoring, Part 1: Run-time performance and availability monitoring for Java systems
http://www.ibm.com/developerworks/library/j-rtm1/

Eclipse Tools

• http://metrics.sourceforge.net/
• http://www.drgarbage.com/
• http://jiprof.sourceforge.net/
• http://www.jcarder.org/
• https://kenai.com/projects/btrace