Question: What is Reference Handler Thread in Java?

1. I suspect it handles running finalizers for the JVM. It's an implementation detail and as such not specified in the JVM spec.
2. This only means that the java.lang.ref.Reference$Lock was locked in the method mentioned in the line preceding it (i.e in ReferenceHandler.run().
3. "Native Method" simply means that the method is implemented in native (i.e. non-Java) code (think JNI).
4. Unknown Source only means that the .class file doesn't contain any source code location information (at least for this specific point). This can happen either when the method is a synthetic one (doesn't look like it here), or the class was compiled without debug information.
5. When a thread waits on some object, then it must have locked that object at some point down the call trace, so you can't really have a waiting on without a corresponding locked.