St. Thomas Aquinas meets the objection head on and answers the problem with his usual razor-sharp efficiency:

<Objection> "It seems that God does not exist; because if one of two contraries be infinite, the other would be altogether destroyed. But the word 'God' means that He is infinite goodness. If, therefore, God existed, there would be no evil discoverable; but there is evil in the world. Therefore God does not exist."

<Answer> "As Augustine says (Enchiridion xi): 'Since God is the highest good, He would not allow any evil to exist in His works, unless His omnipotence and goodness were such as to bring good even out of evil.' This is part of the infinite goodness of God, that He should allow evil to exist, and out of it produce good."

That's the intellectual answer. Now for the practical one.

Respondeo dicendum quod

There are no easy answers. In fact, the problem of reconciling the existence of evil with an all-powerful, omnipotent good God is extremely daunting. It's not impossible, but the answer might not be wholly comforting to a father who lost his only son in a chain of events that seem awfully meaningless. It is emotionally gut-wrenching, and intellectual answers like the one St. Thomas provided may seem too antiseptic, even though it is absolutely reasonable. The argument that answers the problem of evil must be given flesh and blood and not just remain as a intellectual proposition on a page.

The Christian faith does just this, which is why I personally find Christianity to be most the satisfying option available. The reconciliation between the existence of an omnipotent God of goodness and the existence of evil, pain and suffering is found in the Cross. There, we find a story -- a true one -- which is the ultimate realization of the horror that the aforementioned father encounters in the seemingly meaningless death of his only son.

In the eyes of history, it seems like the biggest mistake, the worst practical joke, a meaningless mess of a would-be Messiah whose life ended in a death that even our "advanced" civilization wouldn't subject to a dog.

On the other hand, to the eyes of faith, the Cross was paradoxically the most meaningful act in all of human history. Here was God's sharing into the human condition, a partaking of the loss for a most precious love that a father could ever have.

Paradoxically, in the Cross, evil was answered by justice and mercy, which may seem irreconcilable to our understanding. However, in the act that saw the death of Christ, the barrier between justice and mercy was broken and its fruits were given to humanity as the ultimate answer to the problem of evil. The answer to this problem is not a mere intellectual exercise, but was given a human face -- and that is the face of Jesus Christ.

Thus, the answer given by St. Thomas comes full circle: omnipotent Goodness Himself found a way to produce goodness outweighing the evil in which it was taken from. This Goodness gave the answer to the problem of evil for humanity by becoming one of us and suffering through an evil that summarizes the pain of all humanity, including that of the father today who feels the loss of an only son.

The good news of the Cross is that the death that evil brings was too weak to keep Life incarnate in the grave, but Jesus who is Life burst forth in the Resurrection, which proves that God exists, God is Love and Love is stronger than death. 

Therein lies the hope of fathers who lose their only sons. It's not an easy answer, and it is undeniably painful. But the pain points to an even greater happiness, when "God will dwell with them, and they shall be his people, and God himself will be with them; he will wipe away every tear from their eyes, and death shall be no more, neither shall there be mourning nor crying nor pain any more, for the former things have passed away" (Revelation 21:3-4).

Recommended reading:

Aquinas, Thomas. "Does God exist?" (http://www.newadvent.org/summa/100203.htm), June 24, 2002.

Kreeft, Peter and Ronald K. Tacelli, SJ. Handbook of Christian Apologetics. Downers Grove [IL]: Intervarsity Press, 1994.

see also Solutions to the Problem of Evil by Norman Geisler and others
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For us and our salvation,
Jesus Christ suffered, died, and rose again
so we would believe, repent and be forgiven of our sins.

Vincent Arong