In the episode the various heroes are given code names. "Watchtower" for Chloe as the team coordinator and intelligence asset in homage to the role usually played by The Martian Manhunter for The Justice League in the comics. "Boyscout" for Clark is in homage to a common nickname Justice Leaguers have for Superman, "The Big Blue Boyscout". In the comics Batman gave "Impulse" his code name. Batman meant it sarcastically, hence the joke about how Bart didn't get to choose his own code name.
This is the 11th episode of the season and the start of an annual unofficial tradition where the 11th episode of each season introduces a new character(s), a new hero team or has returning superhero guests. Justice introduces Smallville's version of the Justice League and has a super guest cast consisting of Impulse, Aquaman, Cyborg, and Green Arrow.
Chloe's code name, "Watchtower," is the name of the JLA headquarters. Additionally, Chloe's basing in a clock tower and role as a computer-using coordinator for the team greatly resembles the comic book character Oracle.
Despite using the codename "Impulse", Bart's costume is more of a real world version of the "Flash" costume than the costume Bart wore as Impulse. Aquaman, Cyborg and Green Arrow's costumes are modern day, real world version of the comic book characters.
One of the satellite companies owned by Queen Industries was called JL International, which alludes to Justice League International, what the Justice League was known as for an extended nine year period (1987-1996) in its 50+ year history.
Oliver says that the team's next mission is on the island of Corto Maltese. Corto Maltese is named after a comic book character, created by Italian comic book creator Hugo Pratt; the island has been occasionally referenced in DC Comics since The Dark Knight Returns in 1986.
Bart's interaction with Lex is ironic as Michael Rosenbaum voiced the Flash in the DC Animated Universe. In the Justice League Unlimited episode, "The Great Brain Robbery", the Flash and Lex switched minds and Michael played the animated Lex in the Flash's body.
In the episode, the fake company that Oliver sets up is called 'Artemis Global Consortium'. In the comics, the character of Artemis is often part of the Green Arrow mythos, even appearing in some iterations as a sidekick.