The boundaries between science fiction and fantasy have always been permeable, but sometimes there's a story that feels just like scifi - until you think about it a little bit. And you realize it's pure fantasy.
Here is a handy definition of fantasy, from the venerable Encyclopedia of Fantasy:
When set in this world, it tells a story which is impossible in the world as we perceive it; when set in an otherworld, that otherworld will be impossible, though stories set there may be possible in its terms . . . [but science fiction] tales are written and read on the presumption that they are possible - if perhaps not yet.
Or you can go with the definition that people use on the street: "Fantasy is anything with magic."
Without further ado, here are our top contenders for SF that's really fantasy.
1. Star Wars
How many debates have you had where somebody snarks, "Star Wars is not science fiction - it's fantasy!" Well, that person was right. Not only do the Star Wars movies deal with many of the most common tropes of fantasy, such as an Evil Lord and a Youth With A Quest, but they also contain ample references to "the Force." Even when Lucas brought in the whole midichlorians idea, which I believe was to make the Force seem more scientific by linking it inexplicably to genetics, it's pretty obvious that we're dealing with a non-scientific, spiritual element of the universe that is controlling everything - including who gains power. Despite all the spaceships and aliens, Star Wars at its core is the tale of a boy learning magic to defeat the Evil Lord.
2. Anathem, by Neal Stephenson
It may be set on another planet and involve some of the most outrageously awesome depictions in literature of the scientific process - as well as hyper-realistic space travel - but Anathem's central premise is metaphysical rather than scientific. The "aliens" in the novel are not from another part of the universe, but instead from a dimension which is "less perfect" than those of the main characters. Stephenson tips his hat to many Western metaphysical theories in explaining this conundrum, which is a big hint to the reader that lurking beneath the hard science fictional armor of this plot is a story of cultural progress that relies more on philosophical principles than scientific ones.
3. The Stand, by Stephen King, and The Passage, by Justin Cronin
They're basically the same book, except King's is more lively and weird than Cronin's. A plague hits the Earth that kills most people - in Cronin's novel (the first in a trilogy), the remaining people are turned into A) "vampires" who are compelled to obey the commands of a psychotic killer who is basically patient zero, and B) nice small town folk who begin to hear, psychically, the voice of a perfectly good little girl, who cannot age and remains in a state of innocence and love. It's the classic good vs. evil scenario, and the psychic powers feel more spiritual than scientific. In The Stand, the remaining humans are divided between those who hear the voice of a devil-esque guy in Vegas and a Jesus-esque lady on a nice farm. Both books depict a scientifically plausible end-of-world-via-disease scenario. And both go off into the realm of impossible fantasy and spirituality when they set up their good vs. evil plot structures.
The Dune series, created by Frank Herbert, is an incredible space opera about a highly advanced civilization that refuses to use computer technology. Everything from computation to faster-than-light travel is accomplished via biologically-enhanced humans. In the first novel, our hero Paul drinks worm juice, sees some visions, and becomes the embodiment of an ancient myth among the Fremen, the indigenous people of Dune. Has he simply drunk some kind of natural gene therapy that changes his body and mind? Or is there something metaphysical at work? Especially as the novels develop, it's clearly a lot of both.
5. The Dying Earth
People familiar with this series of novels and stories by hard scifi author Jack Vance won't be surprised that I'm calling it fantasy. The books are full of magic. But I think it belongs on this list because the setting of the stories is pure hard scifi. Earth has entered its twilight days as the sun slowly shrinks and cools. This is a plausible future scenario, and it's one that would indeed change Earth culture profoundly. Would it awaken magic and wizards? Well, that's the fantasy part.
6. "The Call of Cthulhu"
H.P. Lovecraft's mythos surrounding the great tentacled alien Cthulhu is pure science fiction. Aliens came to Earth long before humans evolved, fought wars, and eventually died out - or, in the case of Cthulhu, went to sleep. Things get impossible and fantastical when Cthulhu starts invading everybody's dreams with non-Euclidean geometries and other scary stuff.
7. Dr. Jekyll and Mr. Hyde
Nearly every iteration of this tale, from Robert Louis Stevenson's original novella to Steven Moffat's miniseries Jekyll, begins in a scientifically plausible way. Which is to say, they always start with a scientist in the lab. Jekyll drinks a substance he's invented, and turns into an evil version of himself (or, in some movies, a female version). And yet this classic tale of mad science is pure fantasy for the same reason The Stand is. It deals with metaphysical ideas of good and evil, and how they are at war within humanity. As nice as it would be to identify "pure evil" in the lab and then work on getting rid of it, we will never be able to do that. It is, as our definition of classic fantasy would have it, impossible.
8. Sphere, by Michael Crichton, and Forbidden Planet
One's a novel from the 1980s and one's a movie from the 1950s, but they are about the exact same thing: A bunch of scientists stumble upon a piece of alien technology that can reach into our minds - our "Id" as Forbidden Planet puts it - and turn our unconscious fears and desires into material reality. Neuroscience has yet to locate an "id" or an "unconscious desire" region of our minds. Will our minds one day control computers? Sure. But will that mean our computers will locate our secret fears and turn them into weird sucker fish and giant toothy beasts? Not plausible.
He's from another planet but his powers are utterly fantastical. The end.
The whole premise of this show is that our two FBI agents, Scully and Mulder, represent (essentially) science fiction and fantasy. Scully always searches for the scientific explanation for everything, and Mulder gets stoned with "medicine men" and seeks aliens who may be angels or something even weirder. Likewise, about half the episodes offer us plausible but bizarre stories, and about half seem to suggest that there is something beyond science in the universe. And yet because the show is set in our world, not an impossible one, let's give it the status of something that appears to be science fiction but is, in the final analysis, really fantasy.