In the final scene with the League running down the stairs in pursuit of the Legion of Doom, the heroes passing are grouped into specific tributes to various generations of DC Comics characters. The first group made up of Hawk and Dove, Question, Creeper, and Captain Atom are all creations of writer/artist Steve Ditko. The second group made up of Stargirl and STRIPE, Crimson Avenger, Shining Knight, and Vigilante are all members of the Seven Soldiers of Victory. The third group which contains Hourman, Doctor Midnite, Wildcat, and Doctor Fate are all members of the Justice Society of America. The fourth group which had Vixen, Steel, Vibe, and Gypsy are all members of the League from the "Detroit" era. The fifth group of Booster Gold, Elongated Man, Fire, and Ice hail from the Justice League International. The sixth group which contains Zatanna, Red Tornado, Black Canary, and Green Arrow are all part of the League's "Satellite" Era that was written by Keith Giffen in the 1980s. Following them are the core Justice Leaguers "Big 7": Superman, Wonder Woman, Batman, Flash, Green Lantern, Hawkgirl, and Martian Manhunter. The last of these shown are DC Comics' greatest characters, Superman, Wonder Woman and Batman. Furthermore, Batman is the last character shown, who was the first character featured in the Bruce Timm/Paul Dini TV superhero franchise as a tribute to close it out. This also results in his being both the first and last Justice League member shown in the show.
The scene where Darkseid lifts Superman up and smashes Superman over his knee is modeled after a scene in the "Knightfall" comics saga where the supervillian Bane broke Batman's back with the same type of attack.
Interesting to note, that possibly due to getting a television series spun-off from "Smallville" at the time (and this series would never get an episode past the pilot), Aquaman, one of the oldest superhero characters from Dc Comics, did not make it into the Series Finale.
In-joke: Batman tells Superman, "Don't you have a tall building to go leap?" In the original Superman cartoons, Superman was described by the narrator as being able to "leap tall buildings in a single bound."
Among the Source Wall faces is that of a Marvel Comics character created by Jack Kirby, who created the New Gods and Darkseid: Galactus.