1:25 - Katuunko (after Dooku outlines the Republic's offer): "Your spies serve you well, Count." Obi-Wan gives a similar assessment to Luke in Return of the Jedi: "Your insight serves you well" [48:02].
3:45 - Yoda (after Lieutenant Thire says they're out of range): "I agree." In Revenge of the Sith, Anakin says, "I agree" twice (once after Obi-Wan says that Anakin is not helping by firing at the buzz droids on his fighter: "I agree, bad idea" [6:04] and once after Palpatine explains that the Jedi would kill the two of them and the senators [1:17:36]). Yoda also says it twice (once to Ki-Adi-Mundi's suggestion that it's Obi-Wan who should confront Grievous [49:09] and once to Obi-Wan's suggestion to turn off the retreat message coming from the Jedi temple [1:30:50]).
4:53 - Katuunko (after Ventress says he "might prefer more than words"): "What do you have in mind?" Han uses the same expression in A New Hope: "Don't worry, Chewie; I think I know what he [Luke] has in mind" [1:12:12], and in The Empire Strikes Back, Leia says basically the same thing when she asks Han, "What'd you have in mind for your next move?" [1:14:52].
6:53 - Battle droid (to Ventress, referring to Yoda): "Don't worry, Supreme Leader, we'll take care of him." "Don't worry" also appears in Attack of the Clones (Anakin tells Padmé, "Don't worry; I've given up trying to argue with you" [1:36:02]), Revenge of the Sith (C-3PO tells Padmé, "Don't worry; I'm sure he'll be alright," referring to Anakin [1:24:00], and a clone trooper tells Bail Organa, "Don't worry; the situation is under control [1:24:35]), A New Hope (Obi-Wan tells R2-D2, "Oh, don't worry; he'll be alright," referring to Luke [30:17]; Han tells Chewbacca, "Don't worry, Chewie; I think I know what he [Luke] has in mind" [1:12:12]; and Han tells Leia, "Don't worry; she'll hold together," referring to the Millennium Falcon [1:34:57]), The Empire Strikes Back (C-3PO tells R2, "Don't worry about Master Luke; I'm sure he'll be alright" [12:45]; Luke tells R2, "Don't worry, R2. We're going! We're going!" [36:07]; and Han tells Leia, "Don't worry" [1:20:04]), and Return of the Jedi (Lando, referring to Han, tells Nien Nunb, "Don't worry; my friend's down there; he'll have that shield down on time" [1:27:18]).
9:37 - Rys: "Where's the General [Yoda]?
Jek: "I don't know, we got separated."
Luke also says "We got separated" (referring to himself and Leia) in Return of the Jedi [1:02:20].
9:45 - Clone trooper (it's unclear which one) (referring to battle droids): "Fall back! There are too many of them!" Captain Panaka says something similar in The Phantom Menace (referring to battle droids): "There are too many of them" [23:25], as does a Jedi youngling in Revenge of the Sith (referring to the clones executing Order 66 at the Jedi temple): "Master Skywalker, there are too many of them" [1:23:40], and a rebel pilot says basically the same thing in Return of the Jedi (referring to TIE fighters): "There's too many of them" [1:35:13].
11:16 - Lieutenant Thire (to Yoda): "What are we gonna do, sir?" During Order 66 in Revenge of the Sith, a youngling also asks this of Anakin: "What are we going to do?" [1:23:43]
11:46 - Super battle droid (hijacked by Yoda to fire on the other droids): "Don't shoot!" C-3PO also says this to Jawas in A New Hope: "Don't shoot! Don't shoot!" [16:27].
13:39 - Yoda (to Rys): "So certain of defeat are you?" His comment to Luke in The Empire Strikes Back (after Luke complains that he and R2 will never get his X-wing out of the swamp) is similar: "So certain are you?" [1:09:00].
14:10 - Yoda (to the clones): "Deceive you eyes can." Obi-Wan gives the same advice to Luke in A New Hope: "Your eyes can deceive you; don't trust them" [1:01:45].
19:27 - Dooku (after Katuunko refuses to join the Separatists): "So be it." Palpatine uses this same expression in Return of the Jedi, after Luke refuses to turn to the dark side: "So be it, Jedi" [1:54:26].