...indistinguishable from magic

Any sufficiently advanced technology is indistinguishable from magic. - Arthur C. Clarke

The concept of gods is something that's been with humans for thousands upon thousands of years, and the concept of magic has been around just as long if not longer. With the true advent of science fiction in the last few centuries, it's become more than tempting to combine elements of the fantastic with this. These can range from expounding on speculative or experimental science, to going into full pseudo-science or combining the tamer edges of fantasy elements. These are done for a number of reasons: they can be for just simple can't-think-of-anything-else reasons, or a deliberate push towards creating something incomprehensible for normal humans within the story. There are examples of this in books, live-action, animation and interactive media. Their usage differs depending on the circumstances, and the will of the writer.

In books, there are several instances of aliens being portrayed as akin to deities. David Brin's entire Uplift saga had the mysterious Precursors, who perpetuated the tradition of the "uplifting" of other species barring a few including humans, and are treated as a divine race due to their advanced technology and seemingly benevolent behaviour. Carl Sagen's original novel Contact relies on the conflict between faith and science for its central plot, with the aliens hiding and discovering messages within concepts in a way that can be associated with magic. Arthur C. Clarke used this several times, as can be inferred from the above quote, one of his three rules. In Clarke's Childhood's End, the Overseers are analogous to demons, and the Overmind is comparable to an Almighty God, although in this case it's a hive mind formed from countless races who have transcended physical existence. That concept of transcendence is a recurring part of this trope,

In films and television, such beings are often visually impressive, and it's often accompanied as with books with some religious undertone. Prometheus, the prequel to the Alien franchise, used religious undertones about creator and creation, and portrayed the alien beings as god-like in both technological ability and their in-their-own-image humanoid form. They also fell into the category of being god-like to the point that their attitude to humans was nothing like our own perceptions. Star Trek used the god-like alien story quite regularly, from the mysterious imprisoned being at the end of The Final Frontier to individual episodes that had non-corporeal aliens with mysterious powers crossing paths with the various crews: one of the most notorious is the hypocritical Q. Many other films use this with varying degrees of success, including The Dark Crystal (god-like in the purest sense, including a classical duality between light and dark), The Fifth Element (which goes right over into the realms of mysticism) and the entire Stargate franchise (that uses the advanced tech get-out clause for aliens posing as Egyptian deities). Doctor Who has increasingly gone for this, and even dabbled during its original run with aliens posing as gods (Pyramids of Mars), being mistaken for or treated as gods (The Daemons), or being on a level where they could be classified as gods in a fantasy setting (Guardians from The Key to Time cycle).

The concept of god-like beings is the most common these days in video games, where the need for spectacular battles is a necessity for any game worth its salt. The entire Xeno metaseries plays with this, from extra-dimensional existences equivalent to deities to super-advanced technologies and even to the concept of surviving a universal rebirth (no major spoilers here, I think). The Mass Effect series treads similar ground to the Uplift books, with the most ancient races possessing abilities comparable with divine beings in mythology and fiction. The Halo universe is also touched by this, even though many aspects are comparable or can be linked to theoretical science, so its intrusion into the concepts of the divine is less prominent. One of the most shameless versions of this scenario is the First Civilisation from the Assassin's Creed franchise; a race who predated humanity who transcended time, physical existence, even the concept of human death through genetic survival. Their abilities are so out there that it's little wonder they were called after human deities. Some less memorable examples include the original version of the Atlans from Tomb Raider, almost everything from the StarCraft series, several elements from the as-of-now aborted Half-Life series, the main cast of Asura's Wrath, and (cheating a little here) the Bionicle franchise.

Now why does this happen? I can't speak for everyone, but I can see several reasons. The most obvious is that it's a way of creating tension without the need to explain in any coherent way. The thrill of the totally unknown can be used, but when embellished with the right trimmings it won't be called out as magical by any but real scientists or scientifically-minded readers/viewers/players. Another common reason is the need to create something quickly, ala a sequel or a new episode in a series, and it provides a tried-and-tested formula for the writers. The other reason is more to do with the kind of story a writer is trying to create: by having god-like beings, you bring into question things like faith, the existence of the divine, the place of mankind in the greater scheme of things, ect. It makes a nice little tribute to humanity's want for the divine, and its ability to turn anything that may have a rational explanation into a mystical other such as St Elmo's fire.

I try to steer clear of it myself, but I won't stop anyone else from using this tactic. Or from enjoying this particular take on the unknowable facets of the universe.