4:05 - Jesse: "The capital is too well armed." During the conference on the Death Star in A New Hope, General Tagge* has a similar line: "The Rebel Alliance is too well equipped" [37:02].
8:49 - Clone Trooper (to General Krell): "Sir, there appears to be a disturbance in hangar nine four." This seems to be a reference to the number of the Millennium Falcon's docking bay in A New Hope, although Han Solo and Obi-Wan Kenobi both pronounce it as one number ("ninety-four") [49:19].
8:54 - Krell: "Trooper, what's going on down there? Trooper? Report, trooper."
Fives: "Uh, yes, sir, everything's fine in the hangar, sir. Nothing's out of control down here."
Krell: "Then why have the alarms been triggered?"
Fives: "Ah, uh, uh, uh, it's just a drill, uh, safety drill, sir."
Krell: "Safety check occurs at 0600. Who authorized this drill?"
Fives: "Uh, we are decrypting the alien hardware, sir, standard operating procedure."
Krell: "Who is this? What's your CT number? Trooper, identify yourself."
Elements of this (particularly Krell's last line) are reminiscent of the conversion that Han Solo has with an Imperial officer in A New Hope [1:15:17].
Han: "Uh, everything's under control. Situation normal."
Officer: "What happened?"
Han: "Uh, had a slight weapons malfunction, but, uh, everything's perfectly alright now. We're fine. We're all fine here now. Thank you. How are you?"
Officer: "We're sending a squad up."
Han: "Uh, uh, negative, negative. We have, uh, a reactor leak here, uh, now. Give us a few minutes to lock it down. Uh, large leak, very dangerous."
Officer: "Who is this? What's your operating number?"
11:50 - Fives: "General Skywalker blew up a droid control ship when he was just a kid, and he told me the trick is hitting their main reactor from the inside." This may be an obvious reference, but I'll note it anyway: Anakin's blowing up the droid control ship occurs near the end of The Phantom Menace. [2:02:32].
14:58 - Fives (upon seeing the space battle): "Whoa! What the?" In Attack of the Clones, an alien on Coruscant makes this same exclamation as he sees Obi-Wan flying through traffic while hanging from a droid [15:08]; Han Solo says it in A New Hope after emerging from hyperspace into a meteor shower [1:03:15], and in Return of the Jedi, a scout trooper says this after being hit by Wicket [1:05:38].
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*It's spelt "Tagge" on the Star Wars website, but in the credits, it's "Taggi."