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.
Contributed by mattwo
Naberius is named after the Marquis of hell, and Amduscia is likewise named after the demon King Amdusias, listed in the Goetia.

Lillipa is named after the Kingdom of Lilliput, and the lillipans are based on the lilliputians, from Gulliver's Travels.

Vopar is possibly named after the Vorpal Sword from the poem "Jabberwocky" in Lewis Carroll's "Through the Looking-Glass, and What Alice Found There", but given the abundance of water on the planet it could also be named after the aquatic demon Vepar.

Oracle seems be a Japanese phonetic anagram of Algol, similar to Ragol from Phantasy Star Online, but substituting a C in place of a G.
Contributed by mattwo
Many of the Event Emergency Quests have music from other Sega Games, such as Sonic Adventure 2, Space channel 5, Burning Rangers and NiGHTS into Dreams.
Contributed by mattwo
Attachment
Possibly as a cross-promotion with Hatsune Miku: Project Diva F, Hatsune Miku and Megurine Luka made a cameo concert appearance in Phantasy Star Online 2 in a limited time event performing the theme of Phantasy Star Portable 2, "Living Universe". The stage where they perform is located in the same place that appeared in "The MMORPG Addicts' Anthem".
Contributed by mattwo