The Clone Wars - S4E21 - "Brothers"

12:54 - Morley (upon entering a shelter and seeing dead junkers):  "What the?"  In Attack of the Clones, an alien on Coruscant makes this same exclamation as he sees Obi-Wan flying through traffic while hanging from a droid [15:08]; Han Solo says it in A New Hope after emerging from hyperspace into a meteor shower [1:03:15], and in Return of the Jedi, a scout trooper says this after being hit by Wicket [1:05:38].

The Clone Wars - S4E20 - "Bounty"

5:21 - The control panel in the cockpit features an-other use of the hexagonal pattern seen in the homestead garage in Attack of the Clones and A New Hope:

9:51 - Dengar:  "Heads up people.  We got company."  Han Solo uses a similar expression in A New Hope:  "Luke, we're gonna have company!" [1:15:46].

11:34 - Dengar (after he falls of the subtram):  "Poodoo."  Sebulba also says this after his podracer crashes in The Phantom Menace [1:09:20].

14:19 - Major Rigosso:  "Over my dead body."  Han Solo uses this same expression in A New Hope [50:42].

The Clone Wars - S4E19 - "Massacre"

2:15 - Mother Talzin (to Ventress):  "And then you will fulfill your destiny and become a true Night Sister."  Emperor Palpatine uses the same expression in Return of the Jedi when he tells Luke, "Now fulfill your destiny, and take your father's place at my side" [1:53:38].

2:54 - Count Dooku (to Grievous):  "Go there, and wipe the witches out, all of them."  Darth Sidious uses the same phrase in The Phantom Menace (talking to Nute Gunray and referring to the Gungans):  "Wipe them out, all of them" [1:44:52].

5:22 - General Grievous (to a battle droid):  "Begin landing our troops."  Darth Sidious says almost the same thing to Nute Gunray in The Phantom Menace:  "Begin landing your troops" [4:46].

16:05 - Mother Talzin:  "Pain, Count Dooku.  You will know terrible pain."  This is similar to what Yoda says to Mace Windu in Attack of the Clones:  "Young Skywalker is in pain, terrible pain" [1:21:27].

The Clone Wars - S4E18 - "Crisis on Naboo"

8:59 - Derrown (in disguise as a senate guard):  "What's your identification number?"

Senate Guard:  "SG 1984."

Derrown:  "Alright, move along, and stay sharp."

This exchange includes three bits of dialogue borrowed from A New Hope:  an Imperial officer asks Han, "What's your operating number?" [1:15:41]; a sandtrooper in Mos Eisley, prompted by Obi-Wan's influence through the Force, tell Luke to "Move along.  Move along." [43:51]; and Han says, "Stay sharp" twice, once to Chewbacca before making the jump to hyperspace away from Tatooine [56:08] and once to Luke shortly before the Death Star's sentry ships attack [1:34:15].

9:28 - Part of the fireworks display is apparently meant to resemble the opening crawl of the features:

10:31 - Hardeen (about his sniper rifle):  "Blast!  It's only good for one shot."  Obi-Wan 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]).

14:06 - Cad Bane (after discovering that Hardeen was Obi-Wan in disguise):  "Something smelled wrong about you from the start."  While not exactly the same, this seems to be an echo of what Leia says to Tarkin in A New Hope:  "I recognized your foul stench when I was brought on board" [57:17].

17:42 - The door opens to reveal Dooku at the end of a banquet table in the same way that Darth Vader is revealed in Cloud City in The Empire Strikes Back [1:28:20].

17:50 - Chancellor Palpatine: "It's a trap!"  Admiral Ackbar says, "It's a trap!" in Return of the Jedi [1:35:03], and Leia says it twice in The Empire Strikes Back [1:39:50].

20:02 - Obi-Wan (to Anakin):  "Are you alright?"  In The Phantom Menace, Anakin asks Qui-Gon, "Are you alright?" [1:17:31] and Padmé asks Anakin, "You alright?" [1:19:06].  In Attack of the Clones, Padmé asks Anakin, "Ani, are you alright?" [50:02], and later a clone trooper asks Padmé, "Are you alright?" [2:05:54].  In Revenge of the Sith, Anakin asks the Chancellor, "Are you alright?"[11:49], and a bit later, Mace Windu asks him, "Chancellor Palpatine, are you alright?" [24:53].  In A New Hope, Luke asks Obi-Wan this [59:16] and Biggs asks Luke [1:46:44], and in The Empire Strikes Back, Luke asks, "Rogue Two, are you alright?" [30:31].  Twice in The Empire Strikes Back, Han asks this with a shortened "You alright?" once to Luke [22:12] and once to Leia [31:39].

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There are brief cues of the Imperial march at 15:18 (when Anakin expresses his anger that the Jedi council lied to him) and 17:31 (when he admits to the chancellor with some disdain that the plan to disguise Obi-Wan wasn't his).

The Clone Wars - S4E17 - "The Box"

3:05 - Yoda:  "Skywalker, a powerful Jedi you are."  He describes Anakin this way while speaking to Luke in The Empire Strikes Back, too:  "Oh, father, powerful Jedi was he" [55:18].

3:25 - Yoda (to Anakin, about Obi-Wan):  "If you leave, help him you could, but his future uncertain is."  He tells Luke something similar in The Empire Strikes Back:  "If you leave now, help them you could, but you would destroy all for which they have fought and suffered" [1:18:05].

7:38 - Hardeen: "Dioxis!  Breathe it, and you're dead."  In The Phantom Menace, Quin-Gon also announces "Dioxis" [5:20].

10:22 - Count Dooku (about Hardeen):  "Impressive."  Vader gives a similar compliment to Luke in The Empire Strikes Back:  "Impressive, most impressive" [1:44:30].

17:53 - Moralo Eval:  "This is not the first time you've saved everybody's skin, Hardeen."  Leia uses the same expression in A New Hope ("Somebody has to save our skins" [1:18:22]), and Anakin uses it in Revenge of the Sith (when he tells Obi-Wan, "Alright, but you owe me one, and not for saving your skin for the tenth time" [24:38]).