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- B-Rank: "Count Pokermans": An obvious Pokémon reference. Succeed, and you get the message "You count them all - Phew...so many more than the first 150..."
- B-Rank: "Fight a Cardboard Robot!": Cardbo is likely an allusion to Danbo, Miura's cardboard robot from the manga series Yotsuba&!
- A-Rank: "Assemble a Silver Monkey" and "Cross the Moat": from the kids' game show Legends of the Hidden Temple.
- A-Rank: "Become The King of Fighters!": The King of Fighters, of course.
- A-Rank: "Capture a Control Point!": Team Fortress 2 reference. When you succeed, "You get an ubercharge and fire your minigun maniacally, yelling 'CRY SOME MORE!'". If you lose, "you charge in recklessly and get mowed down by a sentry gun."
- A-Rank: "Defeat the Army of Darkness": from the movie of the same name. The win message reads "You grab your chainsaw and hack through the walking dead. Groovy!"
- A-Rank: "Diagnose a Patient!": "After messing up four times, you do a lumbar puncture and find out it's actually lupus!" Mess up, and "you get stumped and some snarky guy with a cane fires you."
- A-Rank: "D-d-d-d-d-duel!": Yu-Gi-Oh!.
- A-Rank: "Fight a Giant Briefcase": A giant briefcase crashes in through your roof and yells "Huzzah!"
- A-Rank: "Finish a Theme Song!": "Fighting evil by moonlight..."
- A-Rank: "Find Magic Feathers!": An allusion to Tsubasa Reservoir Chronicle.
- A-Rank: "Get the Cake" and "Protect your Companion Cube": Both references to Portal.
- A-Rank: "Seasons Don't Fear the Reaper": from the Blue Oyster Cult song "(Don't Fear) the Reaper".
- A-Rank: "Switch Golden Idols": References Raiders of the Lost Ark.
- A-Rank: "Take Off Every Zig!": Oh, come on.
- AA-Rank: "Get Your Lame On!": A nod to Yu-Gi-Oh! GX and Judai/Jaden's Catch Phrase.
- AA-Rank: "It Is Dark": You are likely to be eaten by a Gwue.
- AA-Rank: "Outwit a Sicilian When Death is On the Line!": Reference to The Princess Bride, complete with Poisoned Chalice Switcheroo gag.
- AA-Rank: "Rescue the Princess": References Star Wars. By winning, "You save the princess and blow up the Death Star". Lose, and "the princess turns out to be your sister. Ew!"
- AA-Rank: "Find the Ultimate Answer!": Hitchhiker's Guide reference. "What do you mean? 42?!"
- AA-Rank: "Wrestle a Turkish Giant!": Yet another Princess Bride reference.
- AA-Rank: "Win the Race!": The win and lose messages are references to Speed Racer.
- Wasteland: "Hunt the Wampus!": Hunt the Wumpus.
- Wasteland: "Hunt the Rubber Pirates": Reference to Luffy from One Piece.
- "Karate Yes": Replicates the basic training given to Daniel in The Karate Kid. Basically, MC Stripeypants (Urahara) wants you to Wax Off and wash his car.
- "2 B A Master": Named for the first English-language Pokémon theme song. The quest text even reads "You want to be the very best...LIKE NO ONE EVER WAS".
- "Wish Around the World": A reference to the ending them to the Spice and Wolf anime's first season.
- The Tatsuki and Chizuru lookalikes are named Sporty and Scary, named after two of the Spice Girls.
- Venus' (Zetsu) picture looks like that of a Piranha Plant.
- The Paper (Konan) looks like and is named for the codename used by Yomiko Readman of Read or Die.
- When you complete the steps required to get Anonymous (L) to join your party, he cries "We cannot forgive! We cannot forget!", the motto of the internet collective (or not) of the same name.
Most of the jutsus taught by the characters are named directly after the ones that are used by their Naruto counterparts. Of those that aren't:
- Fletch's (Ishida) Archer Style jutsus are named after Heavy Metal bands Dragon Force (video game), Kamelot and Blind Guardian.
- Likewise, Shorty's (Rukia) Kido jutsus are named for Slayer and Iron Maiden, and also one for Metalocalypse.
- When she gets promoted to level 3, Pinky (Sakura) is capable of teaching a jutsu called "This Fist of Mine" (a play on Domon Kasshu's "This hand of mine..." battle cry in Mobile Fighter G Gundam). 
- Mister T (Aizen) has "Lucha Libre: Pity the Fool".
- Scary and Sporty use jutsus called "Harder, Better" and "Faster, Stronger".
- At level 3, Lil' Whitey (Neji) learns Whitey Style: Seven Nation Army.
- The Sho Nuff Elixir. Drinking one gives you "The Glow".
- One of the items you can pick up is a Baka Badge, whose item description reads: "It just says '⑨'. Huh?" 
- At the "Billy Idol" event, a group known as MikuMiku Douga comes on stage to sing for the crowd, and the lead singer - a skinny girl with long green hair - is modeled directly after Miku Hatsune.
The following anime- and video game-inspired beasts can cause frustration and major damage to your village if you don't defeat them quickly enough:
- Crazed Mimigas
- Drift Racers
- Fayt is a player designed kaiju based on his own character in the game.
- Ghosts in the Machine
- Go players
- a Metal Idol
- Nine Thousands (formerly Super Saiyans)
- Sexy Lady Cops
- Storm Riders
- Zodiac Girlyboys
- If you and your village are able to survive on a Zombja map for 28 days, or defeat all of the Zettas and seal off the gate, you will receive a trophy called "28 Dayrolls Later".
- Those who have "Survived the Impossible" get the option to "Be a Hero", giving you a single action protected against the cruelty of the Random Number God for that map. In doing so, you get a message that says "Rule 17 Broken", a nod to Zombieland.
Other Game Elements
- The three different Reaper Blood states one can attain are called Shikai, Bankai, and Cobra Kai.
- At the "Juice" Bar, there are a bunch of different drinks named after BvS characters and elements. One of the listed drinks is Rum, but the input box is disabled, and the flavor text next to it reads: "Where has the rum gone?"