Phantoon made his first appearance in Super Metroid, as one of the four Space Pirates protecting the entrance to Tourian and Mother Brain. Samus fights him in a wrecked ship. Phantoon fights by teleporting at random areas and producing ghostly fire. Eventually, Phantoon's eye opens, giving Samus a chance to shoot at Phantoon. After Samus defeats Phantoon, he disappears and the wrecked ship's power is restored.
Phantoon appears as the true final boss in Metroid: Other M.
When Samus returns to the Bottle Ship to retrieve Adam's helmet, she comes across a bunch of strange creatures emerging out of dark pools. As she was heading towards the Control Room, Phantoon appears in front of her and seeks revenge after being defeated for the first time. Phantoon has definitely shown some significant changes. Phantoon is roughly twenty times bigger than before, is far more powerful, and has a bigger arsenal to fight Samus with. Phantoon summons ghostly hands to attack Samus creates giant pools of darkness around the area, and he shoots homing ghostly fireballs practically non-stop. Phantoon's main weakness is his eye, and after Samus defeats Phantoon, he drifts into space and explodes.
Super Smash Bros.
Super Smash Bros. for Wii U
Phantoon appears as a trophy, based on his design from Other M.
Super Smash Bros. Ultimate
Phantoon appears as a support spirit. His Spirit Battle is against an invisible Inkling on the Frigate Orpheon stage. When equipped, he grants the player immunity to sticky floors.
According to his trophy description in Super Smash Bros. for Wii U, Phantoon can only materialize his head in the physical world. His true form is supposedly a giant.
Concept art from Other M depicts his supposed true form as a giant made of dark mist with two Rage Hands as his actual hands. It's unknown whether this still remains his true form or not.
In Super Metroid, Phantoon's roars sound identical to Titanosaurus.
In the Super Metroid manual, it implies that Phantoon seems to have a connection to Mother Brain as it described by being the Wreck Ship's ghost tapping into Mother Brain's thought-waves or simply a physical manifestation of Mother Brain's consciousness. Since MB is a recreation of Mother Brain, it suggested to also be a physical manifestation of MB's consciousness as well.
While unconfirmed, some theorize Phantoon was behind MB taking over the Bottle Ship, and assumes full control of it after her death until Samus returns and destroys him.