A.I. Is a Crapshoot: *Mother, the originator of all AI, saw that she was replicating too fast, too quickly and that her "children" were eating up too much space and latency on connected networks. So she deployed *Reaper, a mindless program killer that is only supposed to destroy copies of herself. It worked... even after the need to destroy copies of herself was gone, and it went on to hunting down the newer generation of AI. Normally, this would only result in the AI being wiped, but due to upgrades in hardware and software making it incompatible with newer systems, *Reaper, instead, completely destroys the system that the AI lurks on by way of data overflow. And since AI have penetrated all facets of the digital world...
Back from the Dead: *Emilia is crashed by the Reaper at one point, but is resurrected from a core dump.
Brand X: The computers used are "Amie", named after the popular real-world Amiga computer series.
Bilingual Bonus: Both "Amie" and "Amiga" are feminine forms of the word "friend", in French and Spanish, respectively.
Chekhov's Gun: Certain users have their handles start with an asterisk. All of them are artificial intelligences.
Near the beginning of the game, after logging into the Matrix for the first time, a person there talks about a VRAM overflow bug in computers. If you message him about it further, he'll give you the patch for it, which requires closing the entire program and reloading your save. Later, this renders *Delphi's attempts to kick you off the Underground Library mostly useless. You'll still be kicked, but what the patch will prevent/fix is an Interface Screw caused by buffer overflow.
Creator Cameo: The pink-haired, bespectacled girl who graces the Underground Library BBS is Christine herself.
Diegetic Interface: The entire game takes place on an Amie computer, via a browser and e-mail client.
Featureless Protagonist: The only things you definitely know about yourself are your screen name and your real name (if you decided to trust Love and actually enter in your real name, that is).
Foreshadowing: Not for this game, but for Analogue: A Hate Story: AI used to have to physically copy themselves into a compressed file, then delete themselves, in order to transmit them anywhere, due to terrible connection speeds.
Historical In-Joke: The Creeper and *Reaper viruses and their effects sound an awful lot like the Morris Worm. Those names, in addition, are of the first accepted computer worm, and the program that, at least apocryphally, wiped it out. Add in the fact that this game is set in 1988, and the joke is complete.
Interface Screw: A buffer overflow causes this. If you don't upgrade your Amie Workbench and Delphi attacks you with one, your workbench will crash and you can't continue until you patch it.
Painting the Medium: Early in the game, you can download an upgrade for the Amie Workbench. Applying it requires you to literally restart the game itself. The version number on the top will change when you do.
Password Slot Machine: One part of the game has you crack a password with a simplified dictionary attack.
Playful Hacker: Several users and eventually the player take this role. As the game's release page notes, advancing in the game requires you to commit telephone fraud, exploit a buffer overflow, and/or "hack the Gibson".
Two handles are seen one early on one in the credits their names Kiros and Ward
GibsonBBS, in general. It's run by a man named Wintermoot (part of which is a shoutout to 4chan, moot being the creator and maintainer of 4chan). There's even a short discussion on the history of cyberpunk itself.
When *Reaper takes down Lake City Local and *Emilia, the help message *Emilia leaves for you is YOU'RE MY ONLY HOPE
"The Matrix" BBS, the screen of which is a minimalist black background. The AI *Delphi also refers to herself as "Oracle" and uses "child" a lot, on top of being a reference to Greek Mythology.
Lampshaded in the ending, where an AI named *Desdemona writes a short epilogue, of sorts, in the style of the Prince's short speech at the end of Romeo and Juliet, this time bemoaning the tragedy of you and Emilie. Christine Love also includes "with apologies to William Shakespeare".
Shown Their Work: The networks and history of viruses in this game are based on real-life information.