The Legion soul is based on the laser from Gradius. It even fires three as though they were from Vic Viper and the options. Another Gradius reference can be found in Dawn: the Bat Company boss sometimes forms into the shape of a ring-spitting Moai head, a common enemy in the Gradius series.
The Kicker Skeleton enemy that occurs in a single location who wears a Scarf of Asskicking and whose only attack is the Rider Kick. It has a chance of dropping a Red Scarf or an Ancient Belt, and its soul lets you do the kick yourself.
Cagnazzo, Scarmiglione/Skull Millione, and Rubicante/Lubicant are members of the Malebranche from the Inferno.
Being a high schooler and a (reincarnation of a) vampire, Konami couldn't resist making Soma full of Jotaro and Dio references.
The Cagnazzo soul is basically a Stand, complete with the "Ora ora ora!" shout. Other blue souls that manifest entities to protect or assist in battle all pretty much resemble the other known stands.
Blocking with the Final Guard elicits a "Muda!"
Healing himself to full by draining enemies causes Soma to quote Dio when he drained Joseph.
What used to simply be the clock item was turned into a colossal reference. First Soma encounters an enemy with a confusing power that won't let him get near. Then he gains the ability to move through stopped time. Finally he learns to stop time himself. Sound familiar? The series' visual effect is even modeled after the JoJo OVAs. The sequel Dawn of Sorrow extends the resemblance as Soma can throw knives with a red soul during the timestop that will freeze in time as they leave his hands, exactly like Dio does it in Stardust Crusaders. This effect also turns up in Portrait of Ruin when Jonathan uses the Stopwatch and then starts throwing knives.
Kyoma Demon resembles the Hanged Man Stand.
A massive Battle Tendency reference appears in the Chaos Realm, where you can encounter a Skeletal Charioteer in a room that resembles part of the Arena section of the Castle, which has quite a striking resemblance to the chariots used by Joseph and Wamuu in their fight.
Mina takes her name from the heroine of the original Bram Stoker novel (for bonus points, "Hakuba" is as Japanese as they could ever make "Harker" to be).
Bat Company could be a reference to the band Bad Company. The official player's guide even makes a joke about it.
The Poison Fist is a supposed kung fu technique popularized in Japan by 80s manga such as the obscure Kinnikuman spin-off, Tatakae!! Ramenman and Wong from Tekken Chinmi. The game has their anime adaptations' purple color when attacking.
Death's second phase is preceded with animation of him revealing his double-bladed scythe, not unlike Darth Maul revealing his double-bladed lightsaber.
