2 of the characters have baller names referencing other games. Moogle's baller name is "Game & Watch Me" referencing Game & Watch, and Mario's baller name is "The Jumpman", referencing Mario's original name in Donkey Kong.

Before the release of Pokemon Gold & Silver there were rumors about Marill being a mysterious new evolution to Pikachu and Raichu called Pikablu, somehow achievable in Red and Blue. These rumors were nothing more than conjecture by fans due to the lack of information at the time. However, this name actually made it into one of the official Pokemon movie trading cards by Topps. This is despite Marill's actual Japanese name even being mentioned on the official Pokemon website. It was corrected in a later edition of the set, but for a time it only served as fuel for the rumors.

A follow-up to the game was in development but later cancelled in 2001 which went under the codename Hermes. The game was to be a frenetic multiplayer platformer for next-generation consoles and would've used the OpenGL-based engine. The game's lead programmer was Todd Daggert.

Master Higgins is based on former Hudson Soft executive Toshiyuki Takahashi, also known as Takahashi Meijin (or "Master Takahashi"), which is the character's Japanese name.

The name Deponia comes from the German word Deponie, meaning disposal site or landfill.

The song "Give It To Me" is an instrumental in the North American version of the game, while the Japanese version featured lyrics. The lyrics were most likely removed due to their sexual nature.

In Chloe's room, there is graffiti on the wall that says "everybody lies no exceptions". This is a line from the animated MTV series "Daria", based around cynical high-school student Daria Morgendorffer.

The poster in Max's room for "the WINGER and the COW" is clearly based on the cover of the novel "The Catcher in the Rye" by J.D. Salinger.

The 'Eye of Providence' appears frequently around Blackwell Academy, including the girls bathroom, the Prescott Dormitory, and the entrance of the parking lot.

The 'Eye of Providence' is an ancient symbol that originally represented the all-seeing eye of God. It can be found in numerous settings both secular and religious, including the official seals of various cities, the stained glass windows of churches, and the Declaration of the Rights of Man and of the Citizen. In popular culture, however, it has come to represent a variety of conspiracy theories, usually involving Freemasonry or the Illuminati.

Despite the character designs being from the 2007 Animated Film, the game uses the voice actors from the 2003 Series by 4Kids Entertainment.

During the prologue of the game the player can find a hidden iron helmet from The Elder Scrolls V: Skyrim, also made by Bethesda.

The first mission contains a vending machine that offers Nuka-Cola, along with an image that resembles the iconic Vault Boy from the Fallout franchise.

Hidden on the sprinkler model are the words "You can't find me." and a picture of a ninja.

The logo of the game's development team, Vicarious Visions, can be seen on the walls of the Egyptian Tomb levels.

In the game, one of the notes mentions that they "sang a bit about not setting the world on fire". This is a reference to the song "I Don't Want to Set the World on Fire" by The Ink Spots, most likely for it's use on the Fallout 3 soundtrack.

In the PS2 version, Ma Chao, Yue Ying, Cao Pi, Zhang He, Taishi Ci, and Ling Tong are given Musou Modes in this version of the game as well as having new weapons and movesets:

• Ma Chao changed from a spear to a great sword (similar to Fu Xi's).
• Cao Pi changed from a short sword to a longsword.
• Zhang He changed from a spear back to his pair of claws.
• Taishi Ci changed from a spear back to his pair of rods.
• Ling Tong changed from a halberd to a three section staff (sanjiegun).
• Yue Ying changed from a longbow to a bladed crossbow.

Zhang He, Taishi Ci and Ling Tong's weapons became their main weapons for future installments.

The song "Spring Of The East" from the games soundtrack was played during the swimming competition of the 2008 Summer Beijing Olympics.

This is the first installment where the English localization properly pronounces Cao Cao's name correctly as "Tsao Tsao" instead of "Kao-Kao".

Because the game was supposed to be a complete revamp for the series, no new characters were added in this installment. In fact, characters Pang De, Xing Cai, Jiang Wei, Da Qiao, Zhu Rong, Meng Huo, and Zuo Ci from the previous installment were omitted, and are only referenced in certain campaigns.

In addition to the cross promotional items and sega-related items, Phantasy Star Online 2 also has a few other references, a few of which might be a result of Konami being a competitor to Sega.

The Duel Gaze is an obvious reference to a Duel Disk from Yu-Gi-Oh! Unlike other talisman weapons in the game, it is apparently strapped to the wielder's arm and is not held by a handle. It also has an unlockable ability called "Trap Activated"(Wana Hatsudo), which boosts the power of ranger traps, in spite of being an techer weapon (albeit one that is equipable by all classes). The Red Duel Gazer likewise has an unlockable ability called "Trap Master" (Takumi wana-shi).

A reference to Metal Gear Solid can be found in the talisman weapon "Metalisolidom", a weapon that is dropped by Transmizer, an enemy which bears an uncanny resemblance to Metal Gear REX. Other Lilipia mechs are also commonly referred to by western players as Metal Gears, though the fact they are on Lilipia might actually be a reference to Laputa from Myazaki's Castle in The Sky which, like Lilipia, is also based on Gulliver's Travels.

While there was an Attack On Titan collaboration, the fight against Magatsu plays homage to it without directly using any of the Attack on Titan material. Instead of 3D Maneuver Gear, the Phantasy Star Crew utilized the previously introduced jump pads, as well as a buff that boosted jump height partway through the first quest where you fight it. Additionally, the trailer/opening featuring Magatsu similarly appears to be a homage to Attack On Titan.