As a game made by fans of both classic and retro games as well as post apocalyptic fiction, there are so many references found in the games. Both towards other post-apocalyptic media and other old-school (or emulating old-school) FPS titles.
- The rocket launcher/flamethrower is called the Master Blaster.
- The second Secret Level in Episode One, "Temple of the Dollar", is a mall. In a theater within said mall, nearly every poster is a joke or reference to the original Doom games or game mods for it. Later, a cardboard cutout of a Mancubus jumpscares you in a videogame store; said store also has a figurine of the Spiderdemon, and Hissywho? as a collectible worth 100 junk.
- Also in the same theater is a torn, faded poster for Mad Max: Fury Road.
- In that same mall, you can find a gym with Vault Boy as its mascot.
- The track "Ghost Town" — that plays in The Wall, Terminus, and during the Modular Epilogue of Episode 2 — is an acoustic remix of "The End Of Doom", by Robert Prince. Similarly, "The Mender Haunts", the theme of the tutorial in 2063 Enriched and the "Temple of the Dollar" Secret Level, is a remix of Prince's "The Healer Stalks". In fact, the switch labeled "Music" (close to the one that opens the exit) tunes the mall's speaker system to the original track.
- In Afterglow, talking to Kyle, a representative of Prosperity's farmers, about the town's chronic crop failures allows you to ask if they've tried rotating their crops. Kyle yells at you for assuming they didn't understand basic farming.
- In the Flooded District of Afterglow, Scav shoots a gong to open a secret door in an Oriental restaurant, and remarks, "Huh. Ancient Chinese secret?".
- When you go to talk to Smiley about the radio you found at the start of 2063, he'll ask you "What're you selling?" You then have the option to tell him "something about that sounded real familiar".
- In Afterglow, one level features a train with wagons from J. Clucks, Duke Burger, Zilla Corporation, and CabalCo. The last one has a familiar set of barrels and a sawed-off shotgun inside.
- In Afterglow, the motorcycle factory you visit in the first hub was owned by a company called Kaneda.
- In Anomaly 210, in Afterglow Scav comments on a radiation gauge by saying "3.6 roentgen... not great, not terrible".
- In the Undercity, there's a masked stalker-like figure, and writing that says "Such is life in the Zone".
- One of the biggest and most important stations in Atlanta, visited in both episodes, is called "Michonne Circle".
- The police station in 2063 has multiple nods to the police station scene from The Terminator, including a front desk that's had a car run into it and a note in the interrogation rooms reminding "1:00 Reese, K".
- One possible line from the militiamen in Michonne Circle is to make fun of "those other idiots" wishing for a nuclear winter.
- In the power plant at the end of Dead Man Walking, you can find workstations that resemble those of Springfield's nuclear plant from The Simpsons, including one with a plaque reading "don't forget: you're here forever".
- In the badlands north of Atlanta, you come across a small town church dedicated to Saint Leibowitz. The psalm of the day is "Forgive me father, I ate a lizard".
- In one secret room in The Gap, the player can find a Fumo dollnote of Zan the Bonebreaker.
- In one location, the player can find the portraits of both Duke and Shelly.
- In a bunker in the Scrapyard area, a contract can be found that plays a familiar tune when picked up and states "Contract accepted. Welcome, Brigador".
- In the Missile Gap, one of the secrets is the corpse of none other than Duke Nukem.
