35:25 - Ahsoka: "So, this is where the fun begins." Anakin also says "This is where the fun begins" at the beginning of Revenge of the Sith [3:47], and Han Solo has a similar line in A New Hope: "Here's where the fun begins" [56:26].
46:02 - It appears earlier, but this is probably the clearest shot of an archway in the monastery:
46:40 - Wilhelm scream (clone trooper)
1:03:59 - Anakin: "Looks like we're gonna have to take this bucket of bolts all the way to Tatooine" references Leia's "This bucket of bolts is never gonna get us past that blockade" in The Empire Strikes Back [35:09].
1:07:19 - Obi-Wan: "If anyone can fly a bucket of bolts through hyperspace, he [Anakin] can" - same as above.
1:10:54 - Anakin: "Hang on back there." Anakin seems to direct this to Ahsoka, but Luke says this to R2-D2 in A New Hope [1:48:52].
1:16:55 - Ziro to an assassin droid: "What is it, Kronos-327?" 327 is a number that frequently appears in Star Wars.
1:27:58 - Ziro to Padmé: "I believe you are too dangerous to be kept alive." In Revenge of the Sith, Palpatine says that Dooku "was too dangerous to be kept alive" [14:38]. Later in the same movie, Mace Windu has a similar line about Palpatine: "He's too dangerous to be left alive" [1:14:23].
1:28:05 - Ziro: "I have powerful friends in the senate" echoes what Leia says to Jabba in Return of the Jedi: "We have powerful friends" [21:02].