3:29 - Father (to Anakin): "Do not underestimate my son." Warnings against underestimation occur twice in Return of the Jedi. Luke tells Jabba, "It's your choice, but I warn you not to underestimate my powers" [24:26], and later Yoda tells Luke, "Luke, do not, do not underestimate the powers of the Emperor" [43:31]. In The Phantom Menace, Nute Gunray advises a battle droid, "These Jedi are not to be underestimated" [10:43], and in A New Hope, Vader tells Tarkin, "Don't underestimate the Force" [1:16:33].
5:25 - Qui-Gon: "Remember your training, Anakin: trust your instincts." This is similar to what he tells him in The Phantom Menace: "Feel, don't think; use your instincts" [57:47].
8:08 - Father (to Obi-Wan): "You cannot interfere!" This is similar to what Obi-Wan says to Luke in The Empire Strikes Back: "If you choose to face Vader, you will do it alone. I cannot interfere." [1:24:25].
9:25 - Anakin's vision of the future includes Obi-Wan's "You were my brother, Anakin" from Revenge of the Sith [2:00:25], Vader's "I hate you" from Revenge of the Sith [2:00:15], and the Death Star's destruction of Alderaan from A New Hope [59:05]:
10:20: Son: "Join me, and together we will destroy this emperor you see in your vision, and we shall end war, corruption, and suffering throughout the galaxy." As in the previous episode, there's a resemblance between this line and what Vader says to Luke in The Empire Strikes Back ("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 what Dooku says to Obi-Wan in Attack of the Clones ("You must join me, Obi-Wan, and together we will destroy the Sith!" [1:33:07]).
11:50 - Anakin (to Obi-Wan): "You will try to stop me." In Revenge of the Sith, after Obi-Wan says, "I will do what I must," Anakin replies with a similar line: "You will try" [1:47:46].
13:43 - Ahsoka: "Mm, nice job." She says this about Obi-Wan's progress in climbing out of a chasm. It's a bit unclear whether she means this genuinely or sarcastically, but if it's the latter, there's a resemblance to Obi-Wan's sarcastic "Good job" about Anakin and Padmé's attempt to rescue him in Attack of the Clones [1:45:00].
20:07 - When the Father dies, he disappears in the same way that Yoda does in Return of the Jedi [45:07]. Obi-Wan's death in A New Hope [1:32:22] is similar but occurs in between shots, not within a single shot.
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Starting around 8:33 during Anakin's conversation with the Son, there's a brief musical cue that's similar to "Battle of the Heroes" from Revenge of the Sith, and there are musical cues of the Imperial march at the end of Anakin's vision and at around 11:44 when Anakin talks to Obi-Wan.