Golden Sun and The Lost Age contain a number of hidden references to popular culture.
- After the episode at Kibombo, the Kibombo warriors stationed at Kibombo Mountains will disappear, making the town of Naribwe south of it breathe a sigh of relief. One woman in town, when Mind Read, says "I'm so glad the Kibombo aren't lurking over us in the hills anymore... They were here, they were there, they were everywhere!" This is likely a reference to the Beatles song "Here, There and Everywhere."
- In Kolima, after freeing the people from Tret, a man on one of the higher floors of one of the buildings, when mind read, says "I'm a lumberjack and I'm okay with that". This is a reference to the British comedy Monty Python's Flying Circus's Lumberjack song sketch, the first line of which is "I'm a lumberjack and I'm OK."
- When entering Alhafra, when the Madran mayor and elder's group arrives in Alhafra shortly after Felix, an old man recites the following: "Haaa hoo hooo... Are we...here? I feel like I just walked 500 miles. I'm fine... I feel like I could walk 500 more!" This is a reference to the lyrics of "I'm Gonna Be (500 miles)".
- In Alhafra, after defeating Briggs but before he escapes, one of Briggs' crew mates says "Everything would have been fine if it hadn't been for you meddling kids!" This is a reference to Hanna-Barbera's Scooby-Doo, Where Are You!, in which every episode ended with the villain uttering some variation of the now-famous catchphrase: "And I would have gotten away with it, if it wasn't for you meddling kids!"
- In the Lucky Medal Fountains from Golden Sun and TLA, there are crabs and turtles that change colour when hit with coins or medals. This may be a reference to the Mario Bros. arcade game, where enemies that have been flipped over will change their colour and move faster if left alone. The animals even resemble common enemies from the game, Shellcreepers and Sidesteppers, which are turtles and crabs, respectively.
Camelot Software Planning, prior to the Golden Sun series, created the well-known Shining RPG and dungeon crawler series, which included titles such as Shining Force. Games such as Shining Force II share many aesthetic similarities with Golden Sun, such as character facial portraits next to text boxes, icon-based menu navigation, and battle scenes where the playable characters' backs are visible on the foreground while they battle the enemies facing them from the background. In addition, there are some easter eggs hidden within Golden Sun games that reference Shining:
- When you first come into Madra in The Lost Age, go to the cave house behind the item shop to see the normal shopkeeper injured in bed. Cast Mind Read to hear her think "Eyes... Shining in the darkness... No! Go away!!!" This references Shining in the Darkness, the first title developed by Camelot Software Planning (then "Sonic! Software Planning") which became one of the first RPGs on the Sega Genesis.
- Shining Force, released after Shining in the Darkness on Genesis, featured a villain named "Darksol" whose goal was to resurrect a monster called the "Dark Dragon", which would serve as Shining Force's final boss. In The Lost Age, the final boss, Doom Dragon, has an offensive monster skill named "Darksol Gasp".