Yes, it is possible to instrument (calls to) custom Java methods and 3rd party libraries. Custom methods are visible on the call stacks and the Java methods performing executions overview.
The ADF Performance Monitor has designed adding custom properties to each request as well. It typically requires no more than one additional line of code per property. Decorating all your page and partial page requests with a custom property is a powerful way to collect events from your software that are not collected out of the box. For example the organisation or department the end-user works for, or the role or type of user the end-user is.