The Clone Wars - S1E21 - "Liberty on Ryloth"

4:29 - Mace Windu:  "This plasma bridge is the only way in or out."  Perhaps coincidentally, this bears some resemblance to C-3PO's comment about the Death Star's cell bay in A New Hope:  "The main entrance seems to be the only way in or out" [1:17.52].

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Among the Twi'lek treasure seen at 12:36 and 19:15, there's an object that resembles the Ark of the Covenant as seen in Raiders of the Lost Ark.

The Clone Wars - S1E20 - "Innocents of Ryloth"

2:07 - Tactical droid (to a battle droid):  "Fire at will."  Palpatine gives the same command in Return of the Jedi:  "Fire at will, commander" [1:14:37].

2:48 - Obi-Wan (to his clone troopers):  "Who's up for a challenge?  We're not getting any reinforcements until those guns are out of commission."  Palpatine uses a similar expression in Revenge of the Sith (referring to Obi-Wan's battle with Grievous):  "We can only hope that Master Kenobi is up to the challenge" [1:02:05], and Han uses the phrase "out of commission" twice in A New Hope:  "I just hope the old man got the tractor beam out of commission" [1:31:37] and "I hope that that old man got that tractor beam out of commission, or this is gonna be a real short trip" [1:32:55].

13:28 - Boil (to Numa):  "Don't cry, kid.  We'll keep you safe.  I- I promise."  In The Phantom Menace, Obi-Wan tells Anakin, "You will be a Jedi; I promise" [2:07:43], and in Revenge of the Sith, Padmé tells Anakin, "I'm not gonna die in childbirth, Ani; I promise you," and he replies, "No, I promise you" [53:46].  Later, Anakin also tells her, "Things will be different; I promise" [1:29:13].

14:26 - Waxer (to Boil):  "How're we gonna explain all this?"  In A New Hope, Luke similarly wonders, "How am I ever gonna explain this?" [36:30]

13:59 - Tactical droid (referring to the Republic troops):  "They are on the move."  Probably just coincidentally, Obi-Wan uses this same phrase in A New Hope to describe the sand people:  "They're on the move" [32:29].

17:42 - Obi-Wan (to Cody as Waxer, Boil, and Numa emerge from a hole in the ground):  "Don't shoot."  C-3PO also says this to Jawas in A New Hope:  "Don't shoot!  Don't shoot!" [16:27].

21:49 - Tactical droid:  "You lose, General Kenobi."  Grievous also says this to him in Revenge of the Sith [20:36].

The Clone Wars - S1E19 - "Storm over Ryloth"

0:32 - This shot, which is re-used from the beginning of "Rookies," copies a shot from the end of Attack of the Clones [2:13:51].

6:14 - A vulture droid crashes into the bridge of the Jedi cruiser in the same way that an A-wing crashes into the bridge of the Super Star Destroyer in Return of the Jedi [1:59:05], although without such disastrous results.

There's a similar shot in "Jedi Crash" [0:21], so similar in fact, that it seems that Anakin and Yularen were simply taken out of this shot from "Storm over Ryloth," and it was used in "Jedi Crash" first.

20:19 - This shot of Anakin's escape pod visually parallels a shot of R2-D2 and C-3PO's escape pod in A New Hope [7:22]:

The Clone Wars - S1E18 - "Mystery of a Thousand Moons"

5:36 - Anakin:  "Obi-Wan and I can handle it."  This has some similarity to Obi-Wan's "Anakin and I can handle this" in Attack of the Clones [2:03:07].

12:34 - Obi-Wan:  "Those are the roots we're looking for."  He uses the same expression in Attack of the Clones ("I have a strong feeling that this bounty hunter is the assassin we're looking for" [57:35] and in A New Hope ("These aren't the droids you're looking for" [43:40]).

12:45 - Obi-Wan:  "I have a bad feeling about this."