The past perfect subjunctive is used in three main ways:

To express subjectivity in the past after the same verbs, impersonal expressions, and conjunctions as the present subjunctive:

Quería que tú lo hubieras hecho.
I wanted you to do it

To express a wish that something had happened differently in the past:

Ojalá que hubiera ido.
I wish he had gone.

In conditional sentences (si clauses):

Si hubiera sabido, habría ido contigo.
If I had known, I would have gone with you.

Let's look at some example sentences:

Hablas como si no hubieras asistido al concierto de Nîmes.
You talk as if you had not attended the concert of Nîmes.

Aunque hubiera ruido se quedarían.
Although there had been noise they would stay.

Si hubiera dedicado más tiempo a estudiar, ya habría sabido decir muchas cosas en español.
If I had dedicated more time on studying, I would have known how to say many things in Spanish by now.

Si le hubiera propuesto un trabajo (puesto), lo hubiese aceptado.
If he had offered him a job, he would have accepted.

Ojalá hubiera preparado las oposiciones.
I wish I had studied for the entrance exam.