Darkrai is likely based on Phobetor, the greek god of nightmares who had the ability to appear in dreams; however, he chose to show up in the form of an animal or even a monster. He often played on people's greatest fears.
Giratina is is inspired by a Japanese tale, "My Lord Bag of Rice." Seta is a giant centipede that is killed by the hero. The Centipede had eyes that glowed like fire and was so big that it's body wrapped around Mount Mikami seven times.
Based on the Hebrew legends of Behemoth & Leviathan, the unconquerable primal masters of land and sea. Just as Groudon is in conflict with Kyogre, it was said that at the end of time Behemoth and Leviathan will battle to the death.