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."
---
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.