How do I know when to cross myself during Mass (Novus Ordo)? I've been going to Catholic (Latin Rite) Mass my whole life and am constantly surprised by the different times that people will cross themselves during the Liturgy.

I only do it when the Priest says the "Father, Son and Holy Spirit"  (and I try to hang on to Holy....Spirit for as long as it takes for him to finish the sentence (not sure if that's necessary).  And doing the three crosses before the Gospel is read (which wasn't certain is in the rubrics but asked about here and found it to be) 

I've seen people cross themselves during the Penitential Rite, the Kyrie, and at other times during the Eucharistic Prayer. And crossing themselves at a Mass with the Bishop when he comes down the aisle blessing everyone (regardless of whether he has holy water).  Is that just how we catch his blessing? People also cross themselves after receiving communion, but as a Catechist, I was taught this is not right, so I'm not asking about that. see this question 

I'll probably ask a follow up about crossing thyself during the Liturgy of the Hours, so no need to include that in the answer.
How do I know when to cross myself during the Mass of Pope Paul VI (Novus Ordo)?

To start with, prior to Mass, we bless ourselves with Holy Water at the entrance of the church by dipping our fingers in into the Holy Water and making the sign of the cross on ourselves. 

The same is done when exiting the church after Mass.


  
  Dipping Your Hand in Holy Water
  
  
  When you come into the church building, what is the first thing you do? Don't, you dip your hand into the holy water and make the sign of the cross? Why do you do that? Well, for three reasons:
        a. in repentance for your sins;
        b. for protection against the Evil One;
        c. to remind you of your baptism.
  
  a. Holy water reminds us to be sorry for our sins. When there is the rite of sprinkling in the liturgy, we always sing the Asperges, which means "you will sprinkle or wash". Asperges me hysoppo et mundabor, lavabis me et super nivem dealbabor. These are words from the great penitential psalm, Ps 50: You will sprinkle me with hyssop and I shall be cleansed: you will wash me, and I shall be made whiter than snow.
  
  b. Holy water is a sacramental which is a protection against the snares of the devil. The old prayer for the blessing of holy water said: "0 God, creator of unconquered power, King of invincible empire and victor ever-great: who put down the powers of hostile dominion and conquer the fury of the roaring enemy, who fight powerfully against our wicked foes: trembling we beseech you, 0 Lord, we implore you and beg you: that you might graciously look upon this creature of water and salt, kindly illumine it, sanctify it with the dew of your loving kindness, so that wherever it is sprinkled, through the invocation of your holy Name, every infestation of the unclean spirit be cast out, and the terror of the poisonous serpent be driven far away. And may the presence of the Holy Spirit deign to be with us always, we who implore your mercy."
  
  c. Holy water reminds us of our baptism: of that great day when we ourselves or our parents or sponsors - renounced Satan, professed faith in Christ, and were baptized into the mystery of the Holy Trinity. At that moment all our sins were forgiven: original and actual, and we became children of God, filii in Filio, heirs of the promise, daring now to call God our Father.
  
  When, you dip your hand into the holy water font, remember these things, and like Our Lady, treasure them in your heart. - Sacred Signs and Active Participation at Mass


During the actual Mass itself we make the sign of the cross at thee different times. All other times the faithful make the sign of the cross are not listed in the norms or guidelines of the Mass and are to be considered optional or due to personal piety either from a personal or regional custom.

When we make the sign of the cross during the actual Mass it is determined by both the rubrics of the Mass and personal tradition.


  How many times are Catholics meant to do the sign of the cross during Mass?
  
  1.The celebrating Priest opens the Mass with a sign of the cross, which the congregation joins in.
  
  2.Just prior to the the Gospel reading there is an older version of the sign of the cross preformed by drawing out a small cross over the forehead, the lips, and the chest.
  
  3.The celebrating Priest concludes the Mass with a sign of the cross, which the congregation joins in.
  
  Optional times:
  
  1.Each time you genuflect you can simultaneously make a sign of the cross (which should be done when you enter Mass, exit Mass, and cross in front of the Altar)
  
  2.When the celebrating Priest passes by during the entering and exiting processions.
  
  3.When a Priest gives a blessing at Mass.
  
  4.After receiving the body and blood of Christ each participant preforms a personal sign on the cross.
  
  5.When you feel moved to “put on the armor of God” 


To this list of options, I would like to add that some priests start their homilies with the sign of the cross which the faithful are encouraged to do also.

In short there are several other times the faithful may make the sign of the cross out of personal piety. 

For those who wish to peruse more information on the subject here is the GENERAL INSTRUCTION OF THE ROMAN MISSAL from the Vatican.