The Clone Wars - S6E13 - "Sacrifice"

13:18 - Anakin (to Yoda):  "We intercepted a transmission calling Dooku to Coruscant."  This line contains the same words that are used in Vader's interrogation of Captain Antilles in A New Hope [5:44].  Vader asks, "Where are those transmissions you intercepted?  What have you done with those plans?" to which Antilles replies, "We intercepted no transmissions."

15:10 - Anakin's encounter with Dooku ends the same way as that in Revenge of the Sith, although the framing doesn't quite match:

19:30 - Force priestess:  "There is another Skywalker."  In Return of the Jedi, Yoda says this to Luke [44:25].

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At 20:54, there's a musical cue of Yoda's theme.

The Clone Wars - S6E12 - "Destiny"

The fortune cookie is "Death is just the beginning."  Probably just coincidentally, this is similar to what Dooku says near the end of his duel with Yoda in Attack of the Clones:  "This is just the beginning" [2:09:49].

4:55 - Force Priestess (Serenity):  "We have been waiting for you, Master Yoda."  Vader greets Obi-Wan the same way in A New Hope:  "I've been waiting for you, Obi-Wan" [1:30:09].

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Starting at 15:10 there's a musical cue of "Battle of the Heroes" from Revenge of the Sith.

The Clone Wars - S6E11 - "Voices"

3:02 - Mace Windu (to Obi-Wan, about Yoda):  "We must keep an eye on our old friend."  The phrase "old friend" is also used in Attack of the Clones (where Palpatine suggests "an old friend, like Master Kenobi" to protect Padmé [6:34] and Count Dooku calls Mace Windu "my old Jedi friend" [1:50:24] and just "old friend" [1:56:05]), in Revenge of the Sith (where Obi-Wan says, "Goodbye, old friend" to Anakin as he leaves for Utapau [51:13] and Yoda refers to Qui-Gon as "an old friend" [2:09:56]), in A New Hope (where Leia sarcastically says, "We, uh, ran into some old friends" when Han asks her and Luke where they've been [1:31:33]), in The Empire Strikes Back (where Yoda says that through the Force, Luke will see "Old friends long gone" [1:17:05]), and in Return of the Jedi (where Luke says, "I have a promise to keep to an old friend" [37:37] and Han calls C-3PO "an old friend of mine" [1:11:53]).

4:37 - Yoda:  "Rest I need.  Yes, rest."  He also says this to Luke in Return of the Jedi [42:02], and the context is similar, too:  both times he's trying to evade the conversation.  Here, he's trying to avoid talking to Anakin about Qui-Gon Jinn's contacting him through the Force, and in Return of the Jedi, he's trying to avoid revealing Vader's true identity to Luke.

6:57 - Rig Nema: "I am not an expert on his biology, but from my point of view, he is in perfect health."  In Revenge of the Sith, Anakin says (to Obi-Wan):  "From my point of view, the Jedi are evil" [1:58:33], and in Return of the Jedi, Obi-Wan justifies himself to Luke by claiming that what he said was true "from a certain point of view" [46:23].

9:46 - Anakin (referring to the induced meditation procedure Yoda is undergoing):  "I don't like this."  This is also Leia's reaction after the Millennium Falcon lands in Cloud City in The Empire Strikes Back [1:19:58].

10:33 - Obi-Wan (to Yoda, after he's out of the induced meditation):  "Welcome back, old friend."  An-other use of "old friend."

10:38 - Yoda:  "Speaking to the dead I was, friends long gone, good friends."  He also uses this description while training Luke in The Empire Strikes Back:  "Through the Force, things you will see, other places, the future, the past, old friends long gone" [1:16:58].

15:22 - Qui-Gon:  "Yoda, my old friend, you have come at last."  Yet an-other "old friend."

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At 2:54, 15:45, and 17:16, there are brief musical cues of Yoda's theme from The Empire Strikes Back, and at 19:40, as Yoda talks about darkness and evil, there's a brief cue of the Imperial march.

The Clone Wars - S6E10 - "The Lost One"

1:16 - Plo Koon (studying the display showing the signal the clone troopers are tracking):  "That is it."  In The Empire Strikes Back, Darth Vader says basically the same thing after seeing an image of the Rebel shield generator that the probe droid sent back, "That's it" [20:56].

16:52 - Silman:  "The Pikes are not to be trusted."  Obi-Wan, speaking to Anakin and referring to Padmé, uses the same expression in Attack of the Clones:  "And don't forget she's a politician and they're not to be trusted" [12:36].

19:17 - Obi-Wan:  "Minister Lom, if you're going to help us, now is the time."  While speaking to Tion Medon in Revenge of the Sith, he says something similar:  "If you have warriors, now is the time" [55:19].