Excel Saga, as one of the premiere gag mangas, makes dozens of references per chapter. The anime, which parodies a different anime genre every episode, makes even more references.
- Ms. Manager is a Captain Ersatz of Emeraldas from Captain Harlock.
- One of the more uncomfortable ones is the whole "human bombs" Shout-Out to Zambot 3. It's still funny, but, for those who know what happens in the show, leaves something of a bad taste.
- The manga spent an entire chapter parodying medical dramas while throwing in references to Black Jack and Resident Evil. It was AWESOME.
- Elgala is the subject of a Fatal Frame parody in volume 20.
- When Elgala starts living with Excel and Hyatt, she sleeps with a giant stuffed Popka doll straight out of Klonoa 2: Lunatea's Veil.
- Elgala wants her short name to be Eh-chan. Excel is already using that. Elgala is designated El-chan. "Why can't you be Ex-chan?" "Some guy on another job is Ex-chan!
- The back cover illustration of volume 17 of the manga is a shout out to the promotional poster for Urusei Yatsura 2: Beautiful Dreamer, with Excel, Miwa Shiouji, and Umi Rengaya in place of Lum, Mujaki, and Baku (respectively) from the original. Also, in volume 12, "Manager" cosplays as Lum (although she claims to be wearing that tiger-striped outfit because she's a fan of the Hanshin Tigers).
- In the English translation by VIZ Media, the sixth chapter of volume 20 was titled "The Waste Land", and had references to The Waste Land in Excel's dialogue. (The original title for that chapter, however, was Kōri no Sekai (World of Ice), according to That Other Wiki.)
- In the fourth chapter of volume 22, Ropponmatsu I now obeys Excel's orders, because she defeated it in combat in the previous chapter. This leads to the following dialogue:
- Earlier in volume 22, there was a several-pages-long Imagine Spot referencing Black Butler.
- In volume 23, in the scene where Elgala discovers that "President Excel", a.k.a. Ropponmatsu I, is a robot, she's wearing the costume of the character Mexiah from the Tenchi Muyo! spinoff Tenchi Muyo: War on Geminar; the costume came from Umi's closet.
- Episode 1: The first scene has a shoutout to/parody of Minky Momo (specifically the episode where the heroine was hit by a truck and died).
- Episode 2:
- In the English dub, Watanabe poses a question using the word "surely". Iwata's response: "Don't call me Shirley; my name's Iwata." — A reference to Airplane!, which codified that gag.
- The episode opens with a Star Wars scroll.
- Episode 3: A parody of the final episode of Cowboy Bebop with Nabeshin and a girl who sounds like a man standing in for Spike and Julia.
- Episode 4: A cameo by Yoda.
- Episode 7: The sewer monster is basically a Xenomorph Queen.
- Episode 12: The episode starts with Nabeshin, in his usual Lupin III-referencing attire, chased by Koshi Rikudo dressed as Zenigata.
- Episode 13:
- Excel briefly turns into Godzilla and fires an atomic ray. She even has a 2000 printed on her tail.
- A clip featuring Nabeshin is the parody of the self-introducing commercial of Lupin III, with Antonio as Jigen Daisuke, the spaceship butler at Episode 2 as Ishikawa Goemon the XIII, Tetsuko-a Metel(from Galaxy Express 999 lookalike women-at Episode 3 as Mine Fujiko, and Mangaka Rikudo as Inspector Zenigata, aka 'Tot-chan' called by Lupin III himself.
- Great Will Of The Macrocosm's self-introduction phrase, "Make love come to the universe, and whole wheat flours bloom!" is the parody of Cutey Honey's catchphrase, "Stars in the heavens, flowers on earth, love in people!", which originated from literature Takayama Chogyū (this catchphrase appears in the first episode of Re:Cutie Honey, too)
- Episode 14: When Ropponmatsu is disarming the bomb, Blossom from The Powerpuff Girls comes out along with electronic scrap.
- Episode 17:
- Episode 19: There's a Lawyer-Friendly Cameo of Nobita from Doraemon.
- Episode 21: Excel has an Imagine Spot with Miss Machiko and her catchphrase "Shameful".
- Episode 22: Space Battleship Yamato, Mobile Suit Gundam, Captain Harlock, and Queen Emeraldas. Also, Excel sings a line from the Martian Successor Nadesico opening in the English dub. This exchange in particular basically sums up the entirety of Leijiverse:
Harlock Stand-In: If a man decides that something must be done, he will accomplish it without another word... no matter how difficult that path may be. Isn't that right, my friend?
Emeraldas Stand-In: When men dream, it's always the women who must make the sacrifice. And yet...
- Episode 23: It's basically a parody of the first episode of Fist of the North Star.
- Episode 25: Nabeshin and his disciples can use an attack called the Name-hame-ha!
- The goofy mecha used by the Daitenzin force is a mix between Giant Robo and the Yatter-wan.