Sephiroth's relationship with Aerith was changed numerous times during the course of production. At some phases they were to be lovers, in others siblings before their relationship was finalized in the final script. Sephiroth's will was also to be used to create an army of monsters that would be born out of crystallized Materia. In another deleted point, when Sephiroth's true body is first seen in the Northern Crater, it would have the contours of a female.

When Cloud is transported to Ivalice by a device called the Celestial Globe in Final Fantasy Tactics, he comes out confused and disoriented. The first thing he says is "The heat! Inside my skull... No, stop... Sephiroth---no!" The Final Fantasy VII boss does not actually appear in the game, though a black-caped swordsman is mentioned.

Many aspects of the final battle with Kefka from Final Fantasy VI are reused in the battle with Sephiroth. Both bosses use Havoc Wing, Heartless Angel, and take on the appearance of angels with dark wings among a backdrop of clouds.

Sephiroth has been a common face in the Gamefaqs user popularity contests. He was the runner-up in the Character Battle II, losing to his nemesis Cloud. He was voted the most popular villain in the Got Villains? contest, beating Ganondorf from the Legend of Zelda series.

Sephiroth has a small cameo in the popular fan parody, Yu-Gi-Oh: The Abridged Series. When the other characters show off their favorite cards, Bakura holds up a card showing Sephiroth from Advent Children, before exclaiming "oops, wrong one", and holding up another.

Sephiroth's strongest weapon in Dissidia is called One-Winged Angel, after his final musical theme.

In Kingdom Hearts Final Mix, the player receives a Keyblade called One-Winged Angel, after defeating Sephiroth. It slightly resembles Sephiroth's Masamune.