The Clone Wars - S1E8 - "Bombad Jedi"

9:43 - C-3PO - "I have a very bad feeling about this."

15:08 - Senator Farr:  "He is our only hope."  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].

18:40 - C-3PO:  "I am a protocol droid on a diplomatic-."  3PO is interrupted by Nute Gunray, but it seems that he was about to say "on a diplomatic mission."  This phrase appears at least twice in A New Hope:  Captain Antilles tells Vader that "We're on a diplomatic mission" [5.55], and later Leia tells him, "I'm a member of the Imperial Senate on a diplomatic mission to Alderaan" [7:58].  Near the beginning of her conversation with Vader, Leia is similarly interrupted when she says, "When they hear you've attacked a diplomatic-" [7:43].

The Clone Wars - S1E7 - "Duel of the Droids"

8:52 - General Grievous:  "I will deal with the Jedi myself."  Grievous uses "Jedi" generically here (he doesn't yet know what specific Jedi have invaded his station), but in Revenge of the Sith, he says, "I will deal with this Jedi slime myself," referring to Obi-Wan Kenobi.  He also has a similar line in "Destroy Malevolence," again referring to Kenobi.  In Return of the Jedi, Vader says, "I will deal with them myself," referring to the Rebel strike force [56:10].

16:19 - Captain Rex:  "I've got a bad feeling about this, sir."

The Clone Wars - S1E6 - "Downfall of a Droid"

5:54 - Anakin:  "I got a bad feeling about this."

The Clone Wars - S1E5 - "Rookies"

0:31 - This shot of the clone army copies a shot at the end of Attack of the Clones [2:13:51]:

4:24 - Clone sergeant: "CT-327, report in. Sentry, do you copy?" Along with an occurrence of 327, there's a resemblance between these lines and what an Imperial officer says in A New Hope: "TK-421, why aren't you at your post? TK-421, do you copy?" [1:08:18]

8:50 - Commander Cody: "I have a bad feeling about this."