The Clone Wars - S1E13 - "Jedi Crash"

0:21 - To some degree, this shot of a Vulture droid crashing into the bridge of a Jedi cruiser visually parallels an A-wing crashing into the bridge of the Super Star Destroyer The Executor in Return of the Jedi [1:59:05].

6:51 - Anakin's life support system makes the same breathing sound that his Darth Vader mask later will.

The Clone Wars - S1E12 - "The Gungan General"

8:55 - Senator Kharrus's staff (first seen at 3:43) resembles the Staff of Ra from Raiders of the Lost Ark:

[source]

This is even the subject of the episode featurette on the Star Wars website:

The Clone Wars - S1E11 - "Dooku Captured"

1:16 - Obi-Wan (after opening the cell door of some prisoners on Dooku's ship):  "Don't bother to get up; you're not the prisoner I'm looking for."  This seems to be a reference to Obi-Wan's line "These aren't the droids you're looking for" in A New Hope [43:39].

The Clone Wars - S1E10 - "Lair of Grievous"

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."

The Clone Wars - S1E9 - "Cloak of Darkness"

8:23 - Clone trooper (to a droid):  "You keep watch here, 327."  And after the droid protests:  "OK, OK, 327-T."