3:12 - Maul (to Savage): "And I shall complete your training, not as your brother but as your master." Vader uses the same expression in The Empire Strikes Back when he tells Luke, "Join me, and I will complete your training" [1:50:39], and the Emperor uses it in Return of the Jedi (also speaking to Luke): "I am looking forward to completing your training" [1:31:04].
7:20 - Maul: "Hondo's base will soon be ours, and he will not survive this." Near the beginning of The Phantom Menace, Rune Haako says something similar as the Jedi cut down battle droids: "We will not survive this" [6:12]. There's also some resemblance to what Palpatine says to Luke in Return of the Jedi: "And your friends on the Endor moon will not survive" [1:44:25].
14:27 - Hondo: "Retreat! Retreat!" Jar Jar also yells, "Retreat! Retreat!" in The Phantom Menace [1:56:53].
18:25 - The cockpit of Maul and Savage's ship features yet more uses of the hexagon design seen in the homestead garage in Attack of the Clones and A New Hope: