Within the game's data is unused audio of Pit saying "I can hardly believe my eyes", followed by Palutena saying, "Set it to your liking". It's likely that this was related to the 3D slider in some way.
There are two unused song segments and various unused dialogue clips, including one clip of Pit saying "Many birds, one BOOM!"
On the Ground stage of The Lightning Chariot, there is a room in which Pit must use jump pads to get over a number of rolling spheres. Pit says that it looks familiar, while Hades says, "I guess the Chariot Master has played Donkey Kong."
In Chapter 17, when Spoiler:Pyrrhon is under the Aurum's control, he says, "01001011010010010100110001001100," which is ASCII binary for "KILL."
In the powers tutorial video, Pit mentions how playing Dr. Mario would help when arranging the power pieces in the grid.
In chapter 5, Pandora's Labyrinth of Deceit, there is an Intensity Gate with a picture of the shop from the original NES Kid Icarus on its wall. Pit will remark about how it "takes him back". It's also worth noting that the player has to be playing on at least an 8 difficulty, referencing how the original Kid Icarus was an 8-bit title.
In Chapter 15, Palutena comments, "I can only tell you that they're not of this world." Pit replies, "You mean they're...invaders from space?!" This is a reference to the arcade game "Space Invaders".
As Pit is shown approaching the entrance of Dyntos' workshop near the end of the Chapter 24 Air Battle, the LucasFilm THX Sound Effect can be heard.
If you tap the Fiend's Cauldron repeatedly before a level, it will get mad, turn around and will occasionally look back at you.
In an early trailer and demo, Pit was voiced by Troy Lund. Lund's voice was replaced with Anthony Del Rio's in the final game.
The Japanese cover art has Pit with his mouth open and smiling, but on the English cover art his face is serious. This is also a common trait of Kirby games, another franchise also created by Masahiro Sakurai.
When the fiend's cauldron spills after the player dies, holding down on the D-Pad will cause a short 8 bit sequence to appear showing the Reaper, and the hearts that have been lost throughout the game.
On Chapter 10 in Kid Icarus Uprising, there is a short fanfare that plays when a puzzle is solved in a lava room. This is almost identical to the puzzle solved fanfare in Metroid Prime.
Komaytos greatly resemble Metroids. Pit acknowledges this during a conversation with Viridi in the Chaos Vortex, though Viridi states that the two are unrelated. Komatoys function similarly to Metroids as they attach themselves to Pit's head and leech health from him. Also, the idol description reads "The last Komaytos is not in captivity, Skyworld is not at peace." This is a reference to the opening of Super Metroid.
During a random conversation between Palutena and Pit when he is wielding a Bow, Pit mentions that a bow was handy in his last "Brawl", to which Palutena will say that she's glad it wasn't a "Melee", which Pit remarks he was never a part of. This is a reference to his debut in Brawl, and when he was considered to being put in Melee, but ultimately was not chosen in favor for the Ice Climbers.
The Idol for the Fairy Orbitars reads "Tired of pixies asking you to listen?" This is a reference to Navi from Legend of Zelda: Ocarina of Time
After the final credits of the game, if the player waits on the "THE END" screen for more than 5 minutes, Hades will have a special speech where he threatens to delete the player's save file and encourages the player to replay the chapters.