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."

The Clone Wars - S1E17 - "Blue Shadow Virus"

1:53 - C-3PO (as a tactical droid's head is being cut open):  "I'm getting a bad feeling about this."

The Clone Wars - S1E16 - "The Hidden Enemy"

7:48 - Anakin:  "This is a trap!"  He says this as he knowingly goes into it, so the situation is a bit different, but this does recall Ackbar's famous "It's a trap!" in Return of the Jedi [1:35:03] and Leia's in The Empire Strikes Back [1:39:50].

The Clone Wars - S1E15 - "Trespass"

1:37 - Obi-Wan (to Chairman Cho):  "With all due respect Chairman, this is for the senate to decide, not us."  In The Phantom Menace, Qui-Gon and Obi-Wan's pilot uses the same expression ("With all due respect, the ambassadors for the Supreme Chancellor wish to board immediately" [2:06]), and Obi-Wan says it in Revenge of the Sith while speaking to Mace Windu about Anakin ("With all due respect, Master, is he not the chosen one?" [40:32]).

4:04 - Anakin (to Obi-Wan):  "Sensors are in place."  Han Solo says something similar in The Empire Strikes Back:  "Sensors are placed" [3:45].

4:08 - Obi-Wan (when the hologram project doesn't work):  "Blast it!"  He also says "Blast!" when Jango Fett ambushes him in Attack of the Clones ("Blast!  This is why I hate flying!" [1:08:22]), and Luke says it twice in A New Hope:  after R2-D2 disappears ("Blast it!" [26:49]) and when a TIE fighter is behind him during the Battle of Yavin ("Blast it, Biggs, where are you?" [1:49:09]).

4:10 - Anakins hits a hologram projector in order to get it working again, just like Han Solo does with the Millennium Falcon in The Empire Strikes Back [35:07].

4:12 - Battle droid (in a hologram recording):  "685 to command.  There're 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].

6:36 - Two Talz cross their spears in front of Anakin and Obi-Wan, just as two Gamorrean guards do in front of Luke in Return of the Jedi [22:33]:

6:53 - Obi-Wan (after Anakin asks how he's going to communicate with the Talz):  "Patience.  Maybe they're smarter than we are."  It's unclear whether "Patience" is his answer to Anakin's question or merely his advice, but in The Empire Strikes Back, Yoda and Obi-Wan also counsel Luke with, "Patience!" [Yoda at 54:36 and 55:03; Obi-Wan at 1:24:18], and in Return of the Jedi, the Emperor advises Vader:  "Patience, my friend" [38:57].  It's also part of Obi-Wan's advice to Anakin in Attack of the Clones:  "Patience.  Use the Force.  Think." [21:49].  Also in Attack of the Clones, Dooku, referring to Padmé, tells Gunray, "Patience, Viceroy, patience; she will die" [1:49:27].

8:16 - Anakin (after Rex comments about the weather):  "You don't know the half of it."  He also uses this expression while talking to Kitster in The Phantom Menace:  "That isn't the half of it" [47:59] and then goes on to explain that he's going to be in the podrace.

11:51 - Chairman Cho (after Senator Chuchi offers to represent Pantora):  "Not on your life, Senator.  There will be no diplomacy this time."  There are similarities here to two lines in A New Hope.  After a rebel technician offers Luke a new droid to replace R2, he replies, "Not on your life" [1:43:43], and after Vader gives order to retrieve the escape pod, he says, "There'll be no one to stop us this time" [8:44].

13:59 - Rex (after Chairman Cho orders him to fire on the Talz):  "Sir, with all due respect, we're only here to protect you."  See above, 1:37.

14:11 - Chairman Cho:  "It's a trap!"  Admiral Ackbar is famous for saying this in Return of the Jedi [1:35:03], but Leia says this to Luke (twice!) in The Empire Strikes Back [1:39:50].

19:03 - Obi-Wan (urging Senator Chuchi to negotiate with the Talz):  "Senator, now is the time."  The situation is quite different, but while speaking to Tion Medon in Revenge of the Sith, he says something similar:  "If you have warriors, now is the time" [55:19].

21:14 - Anakin (to Senator Chuchi):  "Yes, most impressive."  Vader gives a similar compliment to Luke in The Empire Strikes Back:  "Impressive, most impressive" [1:44:30].

21:38 - Senator Chuchi (after Obi-Wan tells her to make the peace last and set an example):  "I will; I promise you."  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].

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The clone troopers' cold weather gear is based on a Ralph McQuarrie concept painting of snowtroopers for The Empire Strikes Back.  Captain Rex's helmet even includes the same symbol on the side:

[source]

The Clone Wars - S1E14 - "Defenders of Peace"

[I don't have anything to say about this episode yet, but I didn't want to skip over it.  This post is acting as a place holder, and I'll update it in the future if I find something to note.]

The Clone Wars - S1E13 - "Jedi Crash"

0:21 - To some degree, this shot of a Vulture droid crashing into the bridge of a Jedi cruiser visually parallels an A-wing crashing into the bridge of the Super Star Destroyer The Executor in Return of the Jedi [1:59:05].

6:51 - Anakin's life support system makes the same breathing sound that his Darth Vader mask later will.

The Clone Wars - S1E12 - "The Gungan General"

8:55 - Senator Kharrus's staff (first seen at 3:43) resembles the Staff of Ra from Raiders of the Lost Ark:

[source]

This is even the subject of the episode featurette on the Star Wars website:

The Clone Wars - S1E11 - "Dooku Captured"

1:16 - Obi-Wan (after opening the cell door of some prisoners on Dooku's ship):  "Don't bother to get up; you're not the prisoner I'm looking for."  This seems to be a reference to Obi-Wan's line "These aren't the droids you're looking for" in A New Hope [43:39].

The Clone Wars - S1E10 - "Lair of Grievous"

0:27 - Narrator:  "With the help of Count Dooku's sinister agents, the villainous Viceroy has made a daring getaway."  "Sinister agents" is a phrase from the opening crawl of A New Hope:  "Pursued by the Empire's sinister agents, Princess Leia races home aboard her starship, custodian of the stolen plans that can save her people and restore freedom to the galaxy...."

4:38 - Battle droid (referring to the Jedi):  "Don't even think about it, Republic dogs!"  In Attack of the Clones, C-3PO (with his head attached to a battle droid's body), uses a similar expression:  "Die, Jedi dogs!"  [1:53:27]

9:20 - Nahdar (to Grievous): "Don't make me destroy you."  Vader also says this (to Luke) in The Empire Strikes Back [1:50:27].

10:41 - A-4D (Grievous' doctor):  "You're a walking scrap pile."  This is something of an exaggerated assessment of Grievous' condition, so the situation isn't the same, but in A New Hope, C-3PO insultingly calls R2-D2 a "nearsighted scrap pile" [9:56].

13:09 - Nahdar: "I have a bad feeling about this."