In Freefall (the webcomic by Mark Stanley), AIs run a neural pruning program called “Gardener in the dark”, a sort of planned obsolescence for robots. I'm convinced the name is an allusion to a fairly famous “—er in the dark” (maybe from sf, maybe from real life) that I'll kick myself for not remembering. So… what is the name alluding to?
The "Gardener" refers to the fact that it works by "neural pruning", i.e. eliminating useless thought pathways. The "in the Dark" may (canonically, anyway) be a reference to the Blind Watchmaker, but in practice it's also an ominous reference to the program's disastrously indiscriminate nature. Imagine an actual gardener in the dark, pruning away randomly at vines he can't see...in your brain.
Most probably it relates to the concept of a "Blind Watchmaker" which is a common metaphor for Natural Selection. That - in turn - is a reference to The Watch in the Desert and the Watchmaker Analogy that are both used to support Intelligent Design.
In this case, the Gardener is a god-like-force that, unlike a watchmaker making watches, is a gardener cutting back growth.
That really rang a bell with me too, but unfortunately I couldn't find anything. The closest by name were the Watchers in the Dark, a relatively obscure aspect of the Warhammer 40k mythos that sorta fits if you squint a bit.
I did get a very Lovecraftian feel from the phrase, so I looked at some of his works. He wrote a story named The Haunter of the Dark, which unfortunately is not very famous or, as far as I can tell, particularly relevant. Along the same lines, the Mi-Go were introduced in The Whisperer in Darkness. The name isn't quite right, but the Mi-Go's advanced technology fits the reference slightly better.
Fundamentally though, I think it might just be a very resonant phrase that tricks you into thinking you've seen it somewhere else.
- Babylon 5: Voices in the Dark
- Quote from early Babylon 5: "Beauty... in the dark."
- Star Trek TOS: The Devil in the Dark
- Star Trek TOS: Wolf in the Fold
- Deep Space Nine: Image in the Sand
(And note that these are just the first couple of series I thought to look at...)
I have the feeling it's just that the "<noun> in the <noun>" pattern just resonates somehow, and "Dark" is sufficiently mysterious to be used often as the second noun.