0:27 - Narrator: "With the help of Count Dooku's sinister agents, the villainous Viceroy has made a daring getaway." "Sinister agents" is a phrase from the opening crawl of A New Hope: "Pursued by the Empire's sinister agents, Princess Leia races home aboard her starship, custodian of the stolen plans that can save her people and restore freedom to the galaxy...."
4:38 - Battle droid (referring to the Jedi): "Don't even think about it, Republic dogs!" In Attack of the Clones, C-3PO (with his head attached to a battle droid's body), uses a similar expression: "Die, Jedi dogs!" [1:53:27]
9:20 - Nahdar (to Grievous): "Don't make me destroy you." Vader also says this (to Luke) in The Empire Strikes Back [1:50:27].
10:41 - A-4D (Grievous' doctor): "You're a walking scrap pile." This is something of an exaggerated assessment of Grievous' condition, so the situation isn't the same, but in A New Hope, C-3PO insultingly calls R2-D2 a "nearsighted scrap pile" [9:56].
13:09 - Nahdar: "I have a bad feeling about this."