At my current project we have almost everything based on .Net. We recently received a Java based application for performance testing. We have Dynatrace but only with .Net licences so we could not use it as APM tool for the Java based application.
I wanted to use standalone HP Diagnostics as APM tool for Java based application but since Micro Focus took over, it is no longer available for free. Earlier standalone HP Diagnostics was free to use.
I had to research about the available open source Java APM tools, that is when I came across Glowroot. It is a very fine free open source Java APM tool. It has very low overhead, it is very easy to install and provides good insights about bottlenecks in your application. In our case it was the threads waiting to get jdbc connection.
Glowroot provides information about which query is taking how much time to execute and you also get to see the thread profile. Glowroot website glowroot.org also has a demo about what all information you can get when you use it. It also allows you to export the slow traces and store as html files.
I would highly recommend Glowroot for your standalone performance debugging of Java based applications.