The Clone Wars - S3E3 - "Supply Lines"

4:49 - Jar Jar:  "Meesa on a diplomatic mission."  The phrase "diplomatic mission" occurs a couple times in A New Hope.  Captain Antilles tells Vader that "We're on a diplomatic mission" [5.55], and later Leia tells him, "I'm a member of the Imperial Senate on a diplomatic mission to Alderaan" [7:58].

The Clone Wars - S3E2 - "ARC Troopers"

2:43 - Lama Su (after Obi-Wan explains that there may be a Separatist attack on Kamino):  "But the Republic blockade is far too strong.  They would not dare."  In The Phantom Menace, Sio Bibble says the same thing after Qui-Gon tells Amidala that the Trade Federation will kill her if she stays on Naboo:  "They wouldn't dare!" [23:36].

4:10 - General Grievous:  "Commence attack!"  Admiral Ackbar has a similar line in Return of the Jedi:  "Commence attack on the Death Star's main reactor!" [1:54:46]

7:49 - Screenshots don't really do this justice, so I won't include them, but this shot of Obi-Wan riding an aiwha and emerging from beneath the ocean is very similar to a shot of a Kaminoan doing the same thing in Attack of the Clones [50:18].

14:31 - Battle droid (knocking on a door):  "Open up!"  This is similar to a situation in A New Hope where a stormtrooper knocks on the door of the room where C-3PO and R2-D2 are hiding and says, "Open up in there!  Open up in there!" [1:17:57], just from the opposite perspective.

14:46 - General Grievous:  "All too easy."  Vader also says this during his lightsaber battle with Luke in The Empire Strikes Back [1:44:18].

The Clone Wars - S3E1 - "Clone Cadets"

3:00 - El-Les:  "CT-782 seems to follow his own path.  He can't do it all alone."  Leia uses this same phrase to describe Han in A New Hope:  "He's got to follow his own path; no one can choose it for him" [1:42:47].

5:05 - Bric:  "If you two would focus on fighting droids as much as you do fighting each other, you might stand a chance out there."  Perhaps coincidentally, this bears some similarity to Obi-Wan's comment to Anakin in Attack of the Clones:  "If you spent as much time practicing your saber techniques as you do your wit, you would rival Master Yoda as a swordsman" [16:30].

8:29 - Commander Colt:  "Start the citadel challenge, version THX, variable 1138."  This is a nod to the title of an-other George Lucas movie, THX 1138.  The number 1138 occurs a number of times in Star Wars.

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Bric's armor is similar to that of General Veers, Dengar, and the snowtroopers in The Empire Strikes Back (as is Moralo Eval's armor in S4E16 - "Friends and Enemies"):

[source]

The Clone Wars - S2E22 - "Lethal Trackdown"

1:48 - Anakin stands at a window in the Jedi temple in the same pose that he stands in on Naboo in Attack of the Clones [59:17] and that Vader stands in on the bridge of his Star Destroyer in The Empire Strikes Back [20:27]:

6:47 - Plo Koon (to Ahsoka):  "We must be cautious."  Obi-Wan also says this (to Luke) in A New Hope [42:44].

20:04 - This quick shot of Aurra Sing's boot adjusting a control on her speeder bike is similar to that of a scout trooper doing the same thing in Return of the Jedi [1:00:14], just horizontally flipped and at a slightly different angle: