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- 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.
- 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 that poem 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 Isekai no Seikishi Monogatari; the costume came from Umi's closet.
- Nabeshin and his disciples can use an attack called the Name-hame-ha!
- The show once did 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. In another episode, when Ropponmatsu #1 dismantles a bomb, Blossom Utonium briefly appears. Oh, and later on, Excel dresses up as both Usagi Tsukino (with whom she shares a voice-actor) and Mickey Mouse.
- Episode four features a cameo by Yoda.
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