Several characters feature the same voices they used in other adaptations. For example, Beast Boy, Starfire and Cyborg all use their Teen Titans voice actors (Greg Cipes, Hynden Walch, and Khary Payton), though Starfire looks and acts differently than in the cartoon (however there are aspects taken from it, such as her speaking imperfect English). Others are voiced by people who have played other DC characters, such as Tara Strong, who returns to voicing Harley(and has her second time voicing Ivy) but not Barbara, and Dean Cain voicing Jonathan Kent (as opposed to Clark). Several characters even have designs based, or directly lifted, from other adaptations (such as Jinx and Beast Boy using their Teen Titans Go! designs).
In "Super Hero High", the security code for the Boom Tube room is "1938". Among other things, 1938 is the year Superman was created. This is especially appropriate, as Waller is showing the room to Supergirl when she enters it.
Supergirl's room is obviously modeled after the Fortress of Solitude.
In "Super Hero High", The Flash is briefly seen running on a treadmill, referencing the Cosmic Treadmill. Also, at one point he dusts a door for fingerprints, referencing Barry Allen's career as a forensic scientist.
Also in "Super Hero High", Giganta is robbing a store called Eclipso Jewels, referencing the DC villain Eclipso, who possesses people through gems.
Harley's pajamas in "Hero of the Year" mimic her classic costume from prior to her New 52 redesign.
Harley's room has some Joker-esque symbols, too, despite his nonexistence here.
In "Spring Prison Break", Killer Frost recounts a story about working for Waller's "Task Force X", the official name of the Suicide Squad, set at Belle Reeve prison and done entirely with an SS team. Most surprising, as given the setting, that team would be furthest from the ones used.
In "Past Times in Super Hero High" the main cast visits an alternate timeline. Alternate Bumblebee remarks Supergirl looks like a student named Power Girl.
In "Out of the Bottle", Supergirl tries to bring an enchanted door down, but it's "tougher than a Kryptonian Thought-Beast".
Supergirl and Batgirl often called themselves "World's Finest Friends", the traditional moniker given to Superman Family/Batman Family team-ups.
In "Finals Crisis" it's revealed that Supergirl had a horse named "Comet", which she used to ride in the Silver Age comics.
While Batgirl's costume is her classic outfit (albeit with her post-New 52 color scheme), her civilian clothing mirrors those of her previous web series incarnation. In addition the overall costume is nearly identical to her first appearance in 60's Batman.
Lena's Evil Plan in the pilot is to trap all the teenagers of Metropolis inside virtual reality. Lex planned on doing this to Superman in Superman 64.
Lena's goal of making an exclusive paradise for kids only is similar to what Morgaine le Fey's son Mordred pulled off (temporarily) in an episode of the Justice League series.
Supergirl's human name (Kara Danvers) and her host parents' names (Jeremiah and Eliza Danvers) are taken from the Arrowverse's Supergirl (2015) version, though it was made that way in the main comics soon afterwards. It's yet to be seen if a version of Alex is part of the equation.
This isn't the first time one of the six main girls here has been involved in gymnastics. Barbara was portrayed as a skilled former gymnast in both The Batman and Batman: The Animated Series, here it's Diana who's on the school's team.
In #MeetTheCheetah Batgirl has a tablet tracking all the girls through the school, a massive reference to Oracle.
Later, in #DCSuperHeroBoys, Bumblebee has created a smartphone app that's called "Oracle".
In #BurritoBucket the three bank robbers have animal masks, meaning they're likely this show's take on the Terrible Trio.
The end credits background has DC-related doodles all around the edges, including one that clearly says "SBFF".
Back in Super Best Friends Forever, Batgirl was hoping to borrow the Invisible Jet to get burritos - this version of Batgirl actually works at a burrito place.
Poison Ivy's civilian identity is a pale, rather sickly-looking girl in a green sweater, much like her initial appearances on Gotham.
Just like in Gotham Girls, Ivy complains about Harley Quinn: "Can't you just [...] like a normal person?!"
#RemoteUncontrolled shows that Ivy and Quinn are sharing an apartment, like they often do in other series and the comics.
One of the items Barbara tries to keep in #PackBat is a can of Bat Shark Repellant. It makes a return in "#LivingTheNightmare", used by Batgirl against sharks in her nightmare.
#SuperSleeper has Batgirl taking a ride on Supergirl's back, again.
A starfish gets stuck on Garth's face in #ShockItToMe, which Livewire hashtags as "#RISEOFSTARRO".
#SuperWho? includes spoofs of The Movie's wrecked-train-tracks and cat-in-tree rescues.
Giganta's sequence highlights multiple large animals on faux screens, most prominently a gorilla. In the comics, Giganta was a mad scientist who first BodySurfed into a Gorilla before kidnapping a strongwoman with Sizeshifter powers and transfering her mind into her body.
Wonder Woman does a series of twirls in her sequence, referencing the old live-action show in which that was how she changed costumes.
Batgirl's is basically an extended rapid-fire series of Batman shout-outs, including the Adam-west style music.
Showing Wonder Woman repeatedly tripping over her own feet has become the way in kids-friendly media to show her abilities are hobbled.
In "#PowerSurge", after the public mistakenly thinks Supergirl has died and Kara decides to just let people think she's dead and come up with a new identity and image, Zatanna tries several new outfits on her, referencing Supergirl's various looks in the comics and animation. Also, when she decides on the Power Girl identity, she identifies herself as Supergirl's Alternate Self from Earth 2, Power Girl's usual origin in the comics.
Mr. Chapin asks Garth (Bernstein), "Do you even have a last name?" In the comics he's never actually had one.
When Batgirl tries busking for bus fare in "#TheCommute", she sings, "Jingle bells, [Robin] smells, [and he] laid an egg...."
#AllyCat: Zee's formal attire has her hair, usually purple, changed to black, which is the main color of hair that other incarnations of Zatanna have.
#PurseScratcher: Selina tries on a pair of smoky-lensed sunglasses that resemble the goggles the character has been associated with since 2001. "I make these look purrrfect!"