3:44 - Obi-Wan: "What in blazes are they [Padmé and C-3PO] doing out here?" echoes Obi-Wan's earlier "What in the blazes is he [Anakin] doing there [on Tatooine]?" in Attack of the Clones [1:22:27].
5:42 - C-3PO: "Oh, we're doomed." He also says "We're doomed" twice in A New Hope [3:04, 16:02], once in The Empire Strikes Back [1:00:38], and once in Return of the Jedi [10:03].
5:47 - Anakin: "Somebody has to save her [Padmé's] skin." Leia has a similar line in A New Hope: "Somebody has to save our skins" [1:18:22], and Anakin uses the same expression in Revenge of the Sith when he says to Obi-Wan, "Alright, but you owe me one, and not for saving your skin for the tenth time" [24:38].
5:52 - Plo Koon: "There he [Anakin] goes again, craving adventure and excitement." This borrows some words from what Yoda says to Luke in The Empire Strikes Back: "Adventure. Heh! Excitement. Heh! A Jedi craves not these things" [56:49].
6:14 - Computer voice: "Welcome to rail jet sub-station nine four." This is a reference to Docking Bay 94 from A New Hope, first mentioned by Han Solo at 49:18.
9:40 - Obi-Wan: "Spinning is not flying."
Anakin: "But it's a good trick."
This is a reference to Anakin's "I'll try spinning; that's a good trick" in The Phantom Menace [1:54:22].
14:25 - General Grievous jumps down behind Obi-Wan Kenobi and says, "Hello, there," the opposite of the situation in Revenge of the Sith [57:27].
15:23 - Grievous: "I will deal with this Jedi myself." He says almost the exact same thing in Revenge of the Sith: "I will deal with this Jedi slime myself" [58:03]. Both times, he's referring to Kenobi. In Return of the Jedi, Vader says, "I will deal with them myself," referring to the Rebel strike force [56:10].
16:15 - C-3PO: "Don't shoot!" He also says this, also with arms raised, in A New Hope [16:27].
17:49 - Obi-Wan Kenobi uses a crane to swing himself behind Grievous on the train, similar to what Indiana Jones does at the beginning of Indiana Jones and the Last Crusade [7:52].