The Clone Wars - S1E1 - "Ambush"

When Lama Su gives Obi-Wan a tour of the cloning facility in Attack of the Clones, he explains, "Clones can think creatively.  You will find that they are immensely superior to droids."  This ability to "think creatively" is subtly demonstrated by Lieutenant Thire in "Ambush."

Roughly halfway through the episode, as Yoda and his squad of clone troopers retreat from a group of destroyer droids, Yoda deflects the droids' blaster fire into a coral branch that then falls on the droids and crushes them.  Later, when Yoda is holding off an-other group of destroyer droids by himself, Thire uses the same sort of technique:  he fires the clones' one remaining rocket at a cliff so that it explodes and the resulting rubble falls on the droids.  He paid attention to Yoda's strategy (taking advantage of his environment) and was then able to adapt it to his own circumstances.

The Clone Wars - S1E1 - "Ambush"

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].

11:00 - Super Battle Droid:  "Die, Republic dogs!"  When C-3PO's head is on a battle droid's body in Attack of the Clones, he has a similar line:  "Die, Jedi dogs!" [1:53:27]

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].