Recommended: Tutorial for Using Java APM with SCOM 2012 R2

I'm a little late to this, but I just found a great introduction if you are looking for a guide to using Java APM from the folks at SCOMfaq.ch. 

• Part 1) Creation & Discovery of Ubuntu Linux VM
• Part 2) Discovery of Java Application Servers
• Part 3) Java APM

December 17th, 2013: Updated Links

If you are looking for a good overview to help you through an installation, this is going to be a great place to start!