What is an overview of "mysteries" in the Catholic Church? In some of my reading on Catholic doctrines, I've noticed that some teachings are clearly explained with rational or moral arguments, and others are called mysteries, that often lack such clear explanations. 

What is an overview of doctrines within the Catholic Church that are "mysteries"?
From this summary of current teaching, the most commonly presented mysteries include:

The Paschal Mystery
The Mystery of the Trinity
The Mystery of the Father (The Mystery of God)
The Mystery of the Incarnate Word
The Mystery of the human person
The Mystery of Original Sin
The Mystery of Incarnation
The Mystery of the Resurrection
The Mystery of Salvation
The Mystery of the Church itself.  


  The Church is a mystery in as much as in her visible reality there is
  present and active a divine spiritual reality which can only be seen
  with the eyes of faith.  


The Church doesn't leave it at that, as each is explored in some depth in both the Catechism and a variety of other documents, but each is classified as a mystery for reasons best left to each topic's details.