The Clone Wars - S2E4 - "Senate Spy"

17:44 - C-3PO: "I'm afraid this situation is quite beyond my capacity."  He also uses the phrase "quite beyond my capacity" in A New Hope.  After convincing Luke and his uncle to buy R2-D2, he tells R2, "Now don't you forget this.  Why I should stick my neck out for you is quite beyond my capacity." [19:30]

The Clone Wars - S2E3 - "Children of the Force"

2:13 - Yularen (referring to hyperdrive rings):  "No, lock them all down!  Hurry!" echoes C-3PO's "No, shut them all down!  Hurry!" about the trash compactors on the Death Star in A New Hope [1:24:18].

17:22 - Mace Windu uses the Force to retrieve his lightsaber from the other side of a closing door, similar to Indiana Jones' retrieving his whip in Raiders of the Lost Ark [9:04].

The Clone Wars - S2E2 - "Cargo of Doom"

10:00 - In the dark, Captain Rex hits his head on a protruding pipe on the Separatist ship.  This seems to be a reference to Jango Fett's hitting his head on the door of Slave I in Attack of the Clones [1:03:23].

12:23 - Anakin:  "Ahsoka, wait; it's a trap!"  Admiral Ackbar says, "It's a trap!" in Return of the Jedi [1:35:03], and Leia says it twice in The Empire Strikes Back [1:39:50].

12:29 - Anakin (referring to Cad Bane):  "Ahsoka, wait; we'll take him together."  In Attack of the Clones, Obi-Wan says, "We'll take him together" to Anakin about Count Dooku [2:04:54].

The Clone Wars - S2E1 - "Holocron Heist"

0:18 - Narrator:  "Jedi trapped on Felucia!  Clones are surrounded by droid forces.  Their only hope is to escape on Republic gunships waiting to land on the embattled surface."  Leia uses the phrase "only hope" twice in A New Hope ("Help me, Obi-Wan Kenobi; you're my only hope" [35:35] and "You must use the information in this R2 unit to help plan the attack; it's our only hope" [1:38:49]); C-3PO uses it once in The Empire Strikes Back ("Your highness, we must take this last transport; it's our only hope" [31:49]); Obi-Wan uses it once, referring to Luke, in Return of the Jedi ("You were our only hope" [47:24]); and Luke uses it once, referring to Leia, in Return of the Jedi ("If I don't make it back, you're the only hope for the Alliance" [1:19:39]). Sio Bibble also uses it in The Phantom Menace: "Our only hope is for the senate to side with us" [23:48].

The Clone Wars - S1E22 - "Hostage Crisis"

3:23 - Anakin:  "When I finished constructing my lightsaber, Obi-Wan said to me, 'Anakin, this weapon is your life.'"  Obi-Wan tells him, "This weapon is your life" in Attack of the Clones too [21:59].