In any literary or artistic field it may seem ridiculous to choose the three greatest works of all time. Yet the attempt can yield results which are worth noting even if they do not convince others.
My choice for the three top SF works are:
A Voyage to Arcturus by David Lindsay (1920).
Last and First Men (1930) and its companion volume Star Maker (1937), by Olaf Stapledon.
The "Ransom" trilogy by C S Lewis, comprising Out of the Silent Planet (1938), Perelandra (1944), and That Hideous Strength (1945).
Any great SF work has qualities which these books don't have; SF is full of territories which authors have made uniquely their own. But to me there is something about these three, some universality of reach, which puts them above even the much-loved achievements of others.
If you know these books you will probably note that I seem to go for those works which have a highly religious or spiritual flavour, and you may ascribe this to bias engendered by my Christian religious beliefs. However, love of literature doesn't work directly in that fashion. For example, one of my favourite authors is the fiercely anti-religious Jack Vance.
In any case the only one of the 3 greatest-evers to be Christian is C S Lewis, and he stresses that his writing is inspired by his visual rather than his religious sense. Perelandra, which describes an unfallen world in which the force of ultimate evil tries to repeat the success it has had on Earth, was inspired initially not by the Book of Genesis but by a science-fictional desire to write about floating islands.
As for the other two, both are non-Christian and in some sense (though not as hostile as Vance), anti-Christian. At any rate they offer rival visions of truth which exclude a religion of love. With Lindsay, grandeur is the thing. His is a Gnostic viewpoint which holds that the world we know was created by the Devil rather than by God, and that our allegiance should be to something completely beyond - something for which he borrows the Norse word "Muspel".
Pleasure of any kind is a humiliating snare devised by the evil God, called Shaping or Crystalman, to distract us from following the only thing worth having - the world of Muspel where grandeur reigns. Not even true love can count for anything; it is a snare like other pleasures.
Stapledon's ultimate value is that of contemplation. The Star Maker, sought by ever more advanced races throughout the history of the universe, is found at last, during the group-mind "Supreme Moment of the Cosmos", to be a creator who is responsible for both good and evil, and stands outside either, using them and all their manifestations as objects of contemplation.
In my agony I cried out against my ruthless maker. I cried out that, after all, the creature was nobler than the creator; for the creature loved and craved love, even from the star that was the Star Maker; but the creator, the Star Maker, neither loved nor had need of love.
But no sooner had I, in my blinded misery, cried out, than I was struck dumb with shame. For suddenly it was clear to me that virtue in the creator is not the same as virtue in the creature. For the creator, if he should love his creature, would be loving only a part of himself; but the creature, praising the creator, praises an infinity beyond himself. I saw that the virtue of the creature was to love and to worship, but the virtue of the creator was to create, and to be the infinite, the unrealizable and incomprehensible goal of worshipping creatures.
A far cry from science fiction, you might say. But in truth I have not, in this article, gone into the science fictional aspects of these books. I have instead concentrated on their ideological frameworks. They all, to some extent, contradict themselves. Stapledon is too human to leave love out of his book or to take the Star Maker's side for long. (Lewis grumbled that Star Maker "ends in pure devil worship" but the point is it doesn't all consist of what it endswith.) Lindsay's spellbinding tale of a journey across Tormance, planet of Arcturus. as Colin Wilson said, "science fiction raised to the nth power". The sheer wonder of discovering and exploring another world has never been evoked like Lindsay evokes it. Yet Lindsay's ideology would have us believe that "there is nothing worth seeing on Tormance". Finally, we come to Lewis himself. He, and the forces of good in his works, are opposed to space travel. His attitude is the not very science fictional one that creatures should stay on their own worlds and not contaminate others with their evils. Yet of course his hero, Ransom, achieves what he does because of his travels across interplanetary space.
It seems the greatest works have the greatest tensions, the greatest contradictions.