The Clone Wars - S3E16 - "Altar of Mortis"

1:42 - Son (to Anakin):  "Join me, and together we can change the balance of the universe, my friend."  Twice in The Empire Strikes Back, Vader says similar things to Luke:  "Join me, and I will complete your training" [1:50:39] and "Join me, and together we can rule the galaxy as father and son" [1:51:45], and in Attack of the Clones, Count Dooku says something similar to Obi-Wan:  "You must join me, Obi-Wan, and together we will destroy the Sith!" [1:33:06].

3:03 - Obi-Wan (to Anakin):  What in the blazes are you talking about?"  He uses this same expression in Attack of the Clones:  "What in the blazes is he [Anakin] doing there [on Tatooine]?" [1:22:27].

6:56 - Obi-Wan:  "Anakin:  always on the move."  He uses this same expression to describe Anakin in Revenge of the Sith too:  "Always on the move" [10:01].

8:02 - Father:  "I am not dead yet."  This seems to be a reference to what Obi-Wan says of himself in A New Hope:  "Oh, he's not dead, not yet" [31:24].

8:12 - Son (to the Father):  "I hate you!"  Vader also says this to Obi-Wan near the end of Revenge of the Sith [2:00:15].

13:07 - Son:  "I have done what is right or what is wrong, depending on your point of view."  This seems to be a reference to either Anakin's "From my point of view, the Jedi are evil" in Revenge of the Sith [1:58:33] or Obi-Wan's "from a certain point of view" in Return of the Jedi [46:23].

18:23 - Anakin screams "No!" after Ahsoka falls.  In terms of masters and apprentices, this is something of the opposite of situations in The Phantom Menace, where Obi-Wan screams "No!" after Qui-Gon is struck down [1:59:48], and in A New Hope, where Luke screams "No!" after Obi-Wan is struck down [1:32:24].  In different circumstances, Vader also screams "No!" in Revenge of the Sith [2:08:43], and Luke does so in The Empire Strikes Back [1:51:30].

The Clone Wars - S3E15 - "Overlords"

0:59 - Anakin:  "Oh, come on.  That's impossible.  Something's wrong.  We're at the exact coordinates where the distress signal originated, but there's nothing here.  Rex is at the exact same coordinates, and he's not here."  In The Empire Strikes Back, Luke also says, "That's impossible" [1:51:21].

1:21 - Obi-Wan (after the shuttle loses power):  "Not good."

Ahsoka:  "Everything's dead, even the life support."

These lines have some similarity to what Anakin says to R2 after they land in the droid control ship in The Phantom Menace:  "Everything's overheated.  Oops, this is not good." [1:58:57].

2:01 - Obi-Wan:  "Everyone strap yourselves in."  Han Solo uses this same expression in A New Hope:  "Go strap yourselves in; I'm gonna make the jump to lightspeed" [56:46].

3:49 - Obi-Wan (in response to Anakin's asking if Obi-Wan or Ahsoka heard Daughter speaking):  "I didn't hear anything."  In The Phantom Menace, Qui-Gon has a similarly dismissive "I don't sense anything" [3:07] in response to Obi-Wan's bad feeling.  The resemblance here, which is probably just coincidental, is more in the delivery than specific diction.  At 3:28, Obi-Wan says, "I don't see anything" after Ahsoka points out a reflection, but this is said in a different manner.

3:57 - Anakin (to Daughter):  "Who are you?"  This too is probably just coincidental, but in The Phantom Menace, Jar Jar Binks has essentially the same line ("Whosa are yousa?" [29:00]) delivered with equal stresses on "Whosa" and "yousa," which is the same way Anakin says it here.

The Clone Wars - S3E14 - "Witches of the Mist"

2:12 - Count Dooku holds two lightsabers to Savage in the same way that Anakin does to Dooku in Revenge of the Sith [14:08], although none of the shots really match:

3:52 - Dooku (to Savage):  "Concentrate."  Yoda also says this (to Luke) in The Empire Strikes Back [1:08:40 and 1:16:38].

4:03 - Savage (to Dooku):  "What you ask is impossible."  Luke says something similar to Yoda in The Empire Strikes Back:  "You want the impossible" [1:11:21].  Moff Jerjerrod, speaking to Vader and referring to the Emperor, has the same complaint in Return of the Jedi:  "But he asks the impossible" [4:21].

4:37 - Savage (to Dooku):  "I hate you!"  Vader says this to Obi-Wan near the end of Revenge of the Sith [2:00:15].

6:50 - Anakin salutes Brother Viscus after he releases him.  Perhaps coincidentally, in Return of the Jedi, Luke gives a similar salute before feigning a jump into the Sarlacc pit [32:32], and Han and Lando salute each other after Han lends the Millennium Falcon to Lando [52:20].

17:22 - Obi-Wan (to Anakin, about Savage):  "We'll take him together."  He also says this (also to Anakin) in Attack of the Clones, referring there to Count Dooku [2:04:54].

The Clone Wars - S3E13 - "Monster"

20:31 - Knox screams, "No!" after his master is struck down.  The same situation is in The Phantom Menace (Obi-Wan and Qui-Gon) [1:59:48] and in A New Hope (Luke and Obi-Wan) [1:32:24].  While the context is different, Vader also screams, "No!" in Revenge of the Sith [2:08:43], and Luke does so in The Empire Strikes Back [1:51:30].