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].