Star Trek: Lower Decks

Mythology Gag in this series.

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General

The opening credits use the same style as Star Trek: Voyager's, only to parody them by having the Cerritos suffer damage in each scene. The theme contains a number of cues from other Trek themes, particularly TNG and Star Trek II: The Wrath of Khan, while the sky-blue typeface is identical to TNG's titles.
Ensign D'Vana Tendi is the second Orion we've seen in Starfleet (although she's the first in the prime timeline; there was Cadet Gaila in Star Trek (2009)).
Rutherford's implant could be related to the technology the Big Bad of the Star Trek: Away Team used for his plans.
Dr T'Ana:
- The last time a Caitian got a speaking role on-screen was also the last time Trek was animated.^note
- She tends to wear a light-blue lab coat, much like Doctor Crusher from TNG, while her attitude evokes Dr. Pulaski from the same series.
One of the promotional posters for the show resembles the poster for the aborted series Star Trek: Phase II, which was eventually turned into Star Trek: The Motion Picture and partially remade as the fan series Star Trek: New Voyages.

Season 1

"Second Contact"

Captain Freeman's mementos include a baseball (like Sisko), an ammonite (like Picard) and a sword (like Calhoun).
Mariner mentions having been to a Klingon prison and fighting a yeti for her boots. Kirk had to deal with a similar experience in Star Trek VI: The Undiscovered Country.
Barnes and Rutherford's walk on the outer hull of the Cerritos recalls Picard and Worf's hull-walk in Star Trek: First Contact.
The shirt of Shaxs' uniform is torn while he fends off infected crewmembers, exposing much of his chest. This is a nod to Kirk's frequent Clothing Damage after a fistfight in TOS.

"Envoys"

The Teaser, in which a glowing light orb flies through the corridors, echoes the opening of the TNG Season 2 premiere, "The Child", along with any number of energy beings from TOS.
Mariner's mumbled sleep phrases, "Buried alive... Marooned for eternity... Moons of Nibia..." are all lines spoken by Khan in Star Trek II: The Wrath of Khan.
K'orin is a Klingon general with an eyepatch, like General Chang in Star Trek VI: The Undiscovered Country.
The SmorgasBorg program is an Unwinnable Training Simulation, essentially the unarmed combat version of the no-win scenario in the Kobayashi Maru test. Furthermore, it has a Punny Name that could easily be mistaken for the Swedish buffet (smörgåsbord), which brings to mind Lily Sloane's comment from Star Trek: First Contact that Borg sounds Swedish. Rutherford is the only person who has beaten the SmorgasBorg, just as Kirk was the only cadet who won the Kobayashi Maru.
Boimler provides a summary of a typical episode in the franchise.
"I should just study bugs on a far-off planet, and then eventually get eaten, and no one will even know until they stumble upon my distress call, but it'll be way too late, and then they'll have to spend a bunch of time deciphering how things went wrong based on my final shaky video logs."

"Temporal Edict"

Boimler muses to himself, "Space: the funnest frontier?" This plays off the famous Opening Narration that began the main titles of TOS and TNG.
Boimler singing "I Love Purgin'" while purging the calibration matrix is reminiscent of Data's "Lifeforms" song while scanning for lifeforms in Star Trek: Generations.

"Moist Vessel"

Captain Durango shares his name with Troi's cowboy character in TNG's "A Fistful of Datas."
Mariner sarcastically performs the Vulcan salute to infuriate Freeman. In Star Trek (2009), Spock offers a sardonic "Live long and prosper" to a minister of the Vulcan Science Academy, which could be interpreted as a subtle Precision F-Strike.
The terraforming fluid has a similar effect to the Genesis device in Star Trek II: The Wrath of Khan.
Ransom performs the "Riker maneuver" by standing on various chairs.
Mariner is seen having to play poker with the rest of the senior staff. Many TNG episodes have the cast playing poker near the start of the episode.
Freeman commands the computer to "Hit it", which is Captain Pike's Catchphrase in Discovery.
Admiral Vassery pronounces "sensors" as "sense-oars", much like Leonard Nimoy did when playing Spock in TOS.

"Cupid's Errant Arrow"

The plot, involving a moon with a decaying orbit, calls back to the threat of the week in the TNG episode "Deja Q".
The teddy bear Boimler hopes to give to Barb is in a yellow uniform with a VISOR, a clear Geordi reference.
Brinson reminisces about travelling back in time to 1920s Chicago, a reference to the TOS episode "A Piece of the Action", although that was due to cultural contamination, not time travel.
She also mentions "reversing the polarity," a technobabble phrase more closely associated with Doctor Who, but employed frequently in Trek as well.
The parasite removed from Boimler's head seems to be inspired by the parasites that took over Starfleet in the TNG episode "Conspiracy".

"Terminal Provocations"

Fletcher had talked a couple Nausicaans out of eating Boimler's heart when they were both cadets; Picard was similarly stabbed through the heart by a Nausicaan during his academy days.
Fletcher plugs his brain into the isolinear core, which is similar to Reginald Barclay connecting his mind to the Enterprise-D's computer in the TNG episode "The Nth Degree."

"Much Ado About Boimler"

The effect used when The Dog transforms is similar to that used whenever Q alters reality.
One of the patients on the Osler is simultaneously ageing and de-ageing, describing himself as "half a rascal"; a reference to the time when Guinan, Keiko, Ro and Picard were de-aged by the transporter in the TNG episode, "Rascals". His appearance is based on the temporal anomaly altered Daniels from the ENT episode "Storm Front", where Daniel's body tissues were existing in a patchwork of different temporal states, from extreme age to extreme youth.
Another unfortunate individual is named "Anthony", a strange catfish-newt that people believe used to be human - a reference to the transformation of Janeway and Tom Paris in the Voyager episode "Threshold".

"Veritas"

The presentation of the "trial" strongly references the trial of Kirk and McCoy in Star Trek VI: The Undiscovered Country, from the placement of the hooded judge with his spark-flinging gavel, the darkened room with the focus characters rising into the chamber win a beam of light, triangular lamps emitting the same color light as the Klingons' tridents, while Clar (voiced by Kurtwood Smith, who played the Federation President in said movie) bears a similar design and role in the proceedings as General Chang.

"Crisis Point"

If not a dig at V, the planet where sentient rats eat sentient lizards might also be a reference to the Kelpians on Star Trek: Discovery, who were used as livestock in the mirror universe.
The opening credits for Mariner's holo-movie mimics the credits for the later seasons of TNG, while the music directly lifts cues from James Horner's Wrath of Khan score.
Mariner says Boimler is "Kind of a Xon to be honest- you probably weren't going to make the final cut." A reference to the Spock replacement character who would have appeared in the aborted Star Trek sequel series, Star Trek: Phase II (which would be reworked into The Motion Picture).
An Overly Long Gag where the bridge crew of the Cerritos take a shuttle up to the ship and spend several minutes circling and admiring it is a reference to a very similar, infamously long scene in Star Trek: The Motion Picture where Scotty pilots Kirk in a shuttle around the Enterprise (the end result of it being converted from the aborted Phase II — a method for recouping the budget). The background music for the sequence is a James Horner-esque take (lots of brass fanfares and sweeping strings) on the series theme.
When the crew walks onto the bridge, there's quite a bit of the infamous Lens Flare used in Star Trek (2009).
The "warp effect" used in Mariner's movie is the same as the one used in Wrath of Khan, and the slight lens distortion on the Mariner before the jump is similar to the warp effect from Star Trek Into Darkness.
Vindicta's name and overly Evil Is Hammy acting approach is reminiscent of Dr. Chaotica from Tom Paris' "The Adventures of Captain Proton" holoprogram on Voyager.
The crash of the Cerritos is similar to the crash of the Enterprise in Star Trek Beyond. It could also call back to the Enterprise-D crashing in Star Trek: Generations.
Vindicta's resurrection mirrors Spock's in Star Trek III.
The signatures at the end of the movie is just like Star Trek VI: The Undiscovered Country.

"No Small Parts"

Ransom name-drops "The TOS Era" (ie, Star Trek: The Original Series) but claims it stands for "Those Old Scientists." Freeman than name-drops the TOS episode "The Gamesters of Triskelion".
The PADD image of the original Enterprise crew on Beta III is drawn in the style of Star Trek: The Animated Series, despite it being a TOS episode.
Ransom cries "They're carving us up like a First Contact Day salmon!"; a reference to Riker crying, "They're carving us up like a roast!" when first encountering the Borg. There may be a meta-joke here as well, since the Pakleds were the first alien race encountered by the Enterprise-D after the Borg; a contrast that has caused some bemusement in the years since.
One of the pieces of junk seen in Mariner's contraband stash is the infamous Spock helmet toy from the 1970s.^note
The Titan's Gunship Rescue is similar to the arrival of the Enterprise-E in Star Trek: First Contact and the Enterprise in Star Trek (2009).
The TNG theme plays during Riker's Big Damn Heroes moment.
Riker comes back from re-living the "original" Archer's Enterprise saying they "Had a long road, getting from there to here", a lyric from the loved-or-loathed soft-rock Star Trek: Enterprise theme.
Peanut Hamper is a parody of the common Trek trope of the newly-introduced guest character with unique powers being the only person who can save the ship from the threat of the week. Rather than saving the day, she declares Screw This, I'm Out of Here!.
- Peanut Hamper’s refusal to put herself in danger is from when the exocomps refused to take a high-risk assignment in TNG’s “The Quality of Life”. The joke about jumping through space references Data’s jump from the Enterprise to the Scimitar in ‘’Star Trek: Nemesis’’.
The show closes on a very meta discussion regarding the fact that Star Trek (ah, I mean Starfleet) tends to focus on first contact and then move on to the next encounter without bothering to follow up.

Season 2

"Strange Energies"

Mariner says, "I know we're not supposed to have interpersonal conflict, but I really hate that Andorian", a reference to Gene Roddenberry's ban on interpersonal conflict in the first season of TNG, which of course created massive problems for the writers vis a vis, well, drama.
Contrary to popular belief, the original series crew never actually encountered a giant, floating disembodied head in space. The closest seen in canon was Nagilum, which was a giant disembodied face encountered by the TNG crew in a pocket-plane. God-Ransom may actually be the first time in Star Trek history in which a ship had to battle a giant, disembodied head.
- However, Ransom's giant hands grabbing ship are similar to Apollo grabbing the Enterprise in "Who Mourns For Adonais?".
Rutherford's confusion of "SMD" with "LSD" might be a call back to Star Trek IV: The Voyage Home, when Kirk confuses "LSD" with "LDS".

"Kayshon, His Eyes Open"

Among the trophies on the Titan are the prototype Enterprise designed by Matt Jefferies for Star Trek: The Original Series and the U.S.S. Titan designed for FASA's Star Trek Tabletop RPG.
At the end of the episode, Boimler tells the other Lower Deckers that being on the Titan felt like “It was a bunch of complex characters thrown into heavily serialized battles, which always ended in mind-blowing twist which made me question the basic tenets of my reality.” This could be seen as a heavy tongue-in-cheek Take That! towards Discovery and Picard's way of storytelling.
Jet says that his supposed additional collar pip was due to a bit of corn, and that any time you see an additional pip on a collar, it's just a bit of corn. A call-back to the days of TNG (and even episodes of Lower Decks itself), in which the less-visible characters often had randomly fluctuating rank insignias.

"We'll Always Have Tom Paris"

The episode is a play on the name of the Star Trek: The Next Generation episode "We'll Always Have Paris"
Boimler refers to the Voyager as the "Voy", referring to the "VOY" production code.
Boimler's fight with the automatic doors is actually a playful nod towards the various bloopers of the cast of the various Trek series dealing with poorly timed door openings, closings and not openings at all as they were operated by hand.
On his way to meet Tom Paris, Boimler hums the Voyager theme.
Star Trek commemorative plates are indeed a thing in our universe.
Mariner and Tendi play dom-jot against a bunch of Nausicaans on Starbase Earhart, just like Picard in the TNG episode "Tapestry".
In her attempt to cover up breaking T'Ana's heirloom, Mariner calls for "Ramming speed!", just like Worf in Star Trek: First Contact.^note
When Rutherford is having his Imagine Spot with the various Shaxs, one of them asks "What was up with T'Pol's hair that one year?" This is in reference to actress Jolene Blalock's wig during the first season on Enterprise, which gave her an odd "helmet hair" look.

"Mugato, Gumato"

The title is a reference to the fact that the Mugato was originally called the Gumato, but got swapped out because Deforest Kelley couldn't pronounce it.
The cannon/holographic program Boimler and Rutherford build resembles the cannon Kirk built in the TOS episode "Arena".
Diplomath appears to be a less-aquisitive version of Tongo.
Mariner compares the Ferengi poachers that captured her and Shaxs as "Last Outpost"-types, referring to the first episode that the Ferengi appeared in.
Honus's description of Mariner ("She's programmed to protect herself at all costs!") echoes Troi's descrition of Roga Danar in "The Hunted" ("He's been programmed to be the perfect soldier... Conditioned to survive at any cost!")

"An Embarrassment of Dooplers"

Boimler and Mariner enter the party with Boimler pretending to be his transporter clone is a less malicious stunt than what Thomas Riker did in the Star Trek: Deep Space Nine episode "Defiant".
One of the side-plots involve Tendi and Rutherford making a model of the Cerritos. Models of popular Star Trek ships have been in production for years.
One of the aliens at the party resembles the original cumbersome design of the Kelpians in Star Trek: Discovery.
When asked to transport bottles of Commander Data bubble bath, Boimler asks if a few are Lores, a reference to Data's Evil Twin, who had a habit of passing himself off as his brother.
- A few of the bottles do indeed have a smirk and a twitchy eye, referencing Lore's famous facial tick.
One of the Vulcans calmly says, "Fascinating", Spock's signature line, upon seeing Boimler and Mariner speed through their ship.
A few Lurians — the species of Morn, the barfly from DS9 — are visible throughout the starbase; one is, naturally, holed up at the bar the Lower Deckers end up at.
Freeman solving the issue by transporting the Doopler ambassador into the snobby party echoes Scotty's decision to beam tribbles over to the Klingon ship at the end of "The Trouble With Tribbles".

"The Spy Humongous"

The promotion club call themselves "red shirts", claiming it makes them sound invincible. This is a reference to the classic Trek staple of the "red shirt" on TOS who would be the one unknown character who would beam down onto a planet and then be immediately killed. The joke plays on the fact that in the TOS era, red shirts were worn by security and engineering personnel, while in the TNG era, they're worn by command.
- The "Red Shirts" also likely double as a reference to the similarly-egotistical "Red Squad" of cadets seen a few times in DS9 (most notably in the episode "Valiant").
Mariner has her face plastered with poisoned barbs from an exotic flower, as happened numerous times on TOS.
Rumdar is convinced to spill the beans about the Pakleds' plans by Captain Freeman the same way Gowron convinced a Pakled to do the same in Star Trek: Klingon.

"Where Pleasant Fountains Lie"

Queen Paolana's treatement of her son echoes Lwaxana Troi's constant attempts to marry off her daughter.
This episode partakes of the common Trek trope of two cast members trapped on a hostile planet and forced to confront one another.
The army that Agimus imagines constructing resembles the Minoan battle robots seen in the TNG episode "The Arsenal of Freedom".
One of the rogue A.I.s seen at the end has the CBS eye logo, showing perhaps, the showrunners' true feelings about their production studio.
The planet of Hysperia might be the same one visited by the Enterprise-D in the TNG novel "Here, There Be Dragons".

"I, Excretus"

The Pandronian Shari yn Yem has a fluctuating number of fingers; sometimes four, sometimes five, just like Ari bn Bem in The Animated Series.
The Terran Empire logo seen in Mariner's test is actually the logo used for the group in Star Trek Online
When the Cerritos is pulled into a black hole, everyone on the bridge experiences trippy after images, similar to the wormhole effect in Star Trek: The Motion Picture.
The list of simulations includes the titles of many Trek episodes ("Time Trap"; "Cause and Effect"; "Natural Selection"; "Evolution"; "Chain of Command"; "Hero Worship" and "Naked Time") and a few, such as "Tribble Troubles"; "Survival of the Fittest", and "From Q to Q", that look like Trek episode titles, but aren't (though "Survival of the Fittest" is the name of a Voyager comic story).
Holo-Shaxs cries out "It's naked time!" again calling out the title of the episode inspiring the simulation.
Boimler's cry that the Borg "Took everything I was!" quotes Picard's breakdown in the TNG episode "Family".

"wej Duj"

The opening title for the episode, "wej Duj", which is Klingon for "three ships", is in Klingon script.
The rock-climbing holodeck simulation is a parody of the beginning of Star Trek V: The Final Frontier.
Boimler says that if Ransom found out he lied, he'd be sent to a penal colony where he'd have to mate with the enemy to start a new civilization, possibly a reference to the TNG episode "Birthright".
The Klingon first officer cries "Klingon blood runs as reddish pink as ever!" referencing its inconsistent coloration over the years.
Like General Chang, the Klingon captain quotes Shakespeare's Julius Caesar: "Cry havoc and let slip the dogs of war!"
The climactic music at the end draws from James Horner's Wrath of Khan score.

"First First Contact"

Continuing with the Star Trek VI: The Undiscovered Country references from last episode:
- The Archimedes is struck by a massive energy wave caused by the destruction of an unstable planetoid. Unlike the Excelsior, it doesn't turn into the wave and the ship is battered.
- Captain Freeman is arrested for supposedly colluding with Klingon extremists in the destruction of Pakled Planet. Kirk was arrested for the death of Chancellor Gorkon, an act performed by Klingon and Federation extremists.
We finally get to see the Cetacean Ops, the oft-mentioned but never seen area of a ship housing whales. It was a discarded idea from TNG that was put in the Technical Manual with the suggestion that whales would be perfect for moving in three-dimensional space.
Ransom controls the stripped down Cerritos by using a joystick, similar to Riker in Star Trek: Insurrection
Ransom flies the ship with a HUD on his EVA suit that breaks when a pebble hits him. it looks alot like the one Kirk and Khan use in Star Trek Into Darkness

Season 3

"Grounded"

When we first see Boimler, we find out his family runs a vineyard, kind of like Picard's as first seen in the TNG episode "Brothers".
The restaurant Tendi and Rutherford is first seen in is "Sisko's", meaning Ben's father most likely expanded just a little.
Speaking of the Siskos, Rutherford is wearing a sweater that looks like one Jake would wear.
We revisit Bozeman, Montana to see that it's a monument/amusement park. The Phoenix ride even uses Steppenwolf's "Magic Carpet Ride".
The Lower Deckers stealing the Cerritos is very similar to what happened to the Enterprise in Star Trek III: The Search for Spock, thankfully not as destructive as that attempt was.

"The Least Dangerous Game"

The Bat'leths and BiHnuchs game is based off of the infamous A Klingon Challenge. The Game Master is none other than (a 24th Century deep-faked) Chancellor Martok, reprised by J.G. Hertzler.
Skydiving down the orbital lift briefly resembles the skydiving to the laser drill scene in Star Trek (2009).

”Mining the Mind’s Mine”

Ransom goes on a tangent about how scientists get their degrees in things like spores and explore the universe only to get eaten by plants, a common fate in many episodes.
Rutherford isn’t the only Black and Nerdy engineer being teased by Dr. Brahms - outside of the various people hooked on holograms, you got Geordi’s infatuation with her.

"Room for Growth"

Freeman getting possessed by a mask is a direct reference to the TNG episode Masks, except she is directly converting the ship instead of the probe slowly generating everything.
Toz is one of the Edosians, the same race as Arex from Star Trek: The Animated Series.
Mariner angrily wishes Delta Shift had gone join the Maquis.
In her explosive rant, Freeman calls Engineering "a bunch of Geordi LaForges".

"Reflections"

The recruitment booth has a tiny model of a Constellation-class and a booth with a TAS-style Kirk and Spock photo booth. Mariner even mentions "the Undiscovered Country".
One of the flirting questions Rutherford asks is if the spots on a Trill go all the way down, the infamous question asked to Jadzia Dax.

"Hear All Trust Nothing"

The episode references the 109th entry of the Rules of Acquisition, which Sisko quotes to Nog when the latter hears of the Romulan Empire signing a pact of nonaggression.
Rutherford hangs himself off the second floor of the Prominade, similar to how Jake Sisko and Nog did. Rutherford also moans that he could have a heart-to-heart with a junior reporter, another Jake reference.
When the Ferengi Dabo dealer taunts Boimler, Boimler replies that "fortune favors the bold", which is what Sisko says in the DS9 episode "Favor the Bold" when he decides to initiate Operation: Return and retake the station.

"Crisis Point 2: The Rise of Paradoxus"

The mysterious Ki-Ty-Ha is revealed to be the preserved Wright Flyer from Kitty Hawk, North Carolina, similar to how V'Ger is revealed to be the Voyager 6 probe. It first appears in the form of a giant rock monster, which was the scripted-but-never-filmed form of the bad guy entity in Star Trek V. (For that matter, Ki-Ty-Ha also sounds a bit like the name of the planet, "Sha-Ka-Ri").
The Melponar sisters are probably a reference back to the Duras sisters, recurring Klingon villains in Star Trek: The Next Generation and Star Trek: Generations.
When Boimler describes part of the plot to Mariner, that the Romulans intend on using Chronogami to rewrite any part of history, Mariner groans they're gonna make a cinematic alternate universe with other people playing younger versions of themselves, a jab at the Kelvin Timeline.
Mariner also sarcastically asks if they're going to have to go back in time to assassinate Kennedy, which was a rejected concept for Star Trek II: The Wrath of Khan.
The Federation science base that developed the "Chronogami" is clearly based on Space Station Regulus I, the birthplace of the Genesis Torpedo also from Wrath of Khan. Everything from the architecture to the scientist uniforms (and the scientist love interest) to that prop with the lasers on top that was in an abundance of 80s movies.
The CGI video on the Chronogami project is based on the Genesis video from Wrath of Kahn, which was groundbreaking in 1982. Rutherford comments on the impressive graphics.
The Australian punks (especially the one with the oversized boombox) are an obvious reference to the punk from Star Trek IV: The Voyage Home.
The plotline of Romulans traveling back in time to sabotage the Federation's history is similar to the Klingons' ploy in the 1985 Pocket novel Ishmael, as well as the Borg's plan in Star Trek: First Contact.
The cinematic uniforms' pants merge seamlessly with their shoes. Just like in the motion picture, they're only clearly visible in a few shots.