The final season three appearance was in episode 15 "The Ogg Couple" where Egghead and Olga steal the Sword Of Bulbul and The Egg Of Ogg.
In "The Entrancing Dr. Cassandra," Egghead (alongside Joker, Penguin, Riddler, Catwoman, and King Tut) was freed from prison by Dr. Cassandra Spellcraft and her husband Cabala, but this brief appearance was by a stand-in.