- A subtle one — Anakin's lightsaber is shaped exactly like the one he'll use as Darth Vader, but with a chrome emitter shroud instead of a black one.
- Early in the film, Obi-Wan is concerned about Anakin, knowing that he's been having dreams about his mother. Anakin says he'd rather dream about Padmé. Next film he does, except just like his mother, it's about Padmé's approaching death.
- During the meeting with the Chancellor and the Jedi Council, when Palpatine pleads with Senator Amidala to accept the protection of Jedi bodyguards Kenobi and Skywalker, he says "Do it for me, Milady. Please? The thought of losing you...is unbearable." This hearkens to Anakin's main motivation in turning to the Dark Side in Episode III, which was in huge part orchestrated by Sidious/Palpatine.
- While outside Padmé's room, Anakin and Obi-Wan discuss trusting politicians, Anakin tells Obi-Wan he thinks Palpatine is a great man.
- "Why do I get the feeling you're going to be the death of me?" — Obi-Wan to Anakin. Two movies later...
- On the political side of the film, Padmé says the people of Naboo wanted the constitution of their planet amended so she could stay in office. Meanwhile, on Coruscant, there's the constitution of the Republic about to be suspended so Palpatine can stay in office.
- Anakin's own views on how the galaxy should be run:Anakin: We need a system where the politicians sit down and discuss the problem, decide what's in the best interest of all the people, and then do it.
Padmé: That's exactly what we do. The problem is the people don't always agree.
Anakin: Then maybe they should be made to.
Padmé: By who? Who's gonna make them?
Anakin: I don't know. Someone.
Anakin: No, of course not me.
Padmé: But someone.
Anakin: [nods] Someone wise.
Padmé: That sounds an awful lot like a dictatorship to me.
Anakin: Well, if it works...
- During the fireplace scene, Anakin tells Padmé about how his feelings for her are causing him agony. Padmé in this scene is wearing a dress with a choker on it. Guess what happens to her in the next movie? Bonus points for this quote from Anakin: "The thought of not being with you...I can't breathe."
- R5-D4, who blows his motivator in episode IV, rolls right by R2-D2 in the opening shot of Tatooine.
- A literal instance happens as Anakin leaves to look for his mother Shmi. His silhouette's head looks like Darth Vader's helmet. And the best part is it just happened that way on set.
- After Anakin slaughters the Tusken Raiders, as he tells Padmé about it, the Imperial March plays for a few seconds.
- R2-D2 and C-3PO, roaming Tatooine, with a message concerning Obi-Wan Kenobi. Sounds familiar...
- A subtle visual involving how the light sabers are Color-Coded for Your Convenience. In virtually every other Star Wars movie, the masters and teachers among the Jedi tend to be the ones carrying the green sabers while students and apprentices (whether they're fully trained or just getting started) carry the blue ones. At the beginning of the movie, both the teacher and the student are carrying blue sabers. (Obi-Wan would later admit to Luke that he felt he'd made a mistake in taking up training Anakin so soon after completing his own training; so maybe this is a hint that he's still more like a peer than a superior to Anakin?) When Anakin and Obi-Wan lose theirs and need new ones, however, Anakin gets a green one and Obi-Wan gets a blue one from the arriving Jedi army. Earlier on, Anakin had been complaining that he felt he'd surpassed Obi-Wan and his teacher was holding him back. Now he's got a teacher's saber and Obi-Wan has a student's. Coincidence? Also, note that in A New Hope, Vader would insist "I am the teacher now" in response to Obi-Wan's last offer to complete his training as a Jedi.
- There's also Count Dooku switching off a hologram of the Death Star plans and taking them with him to keep safe.
- At the very end of the film, the Imperial March plays as Palpatine looks over a mass of Clone Troopers, which is a very interesting use of music to do this.
- Anakin's lightsaber is bisected in half at one point. In the next movie, Anakin himself is bisected, at his legs and hands. As a bonus, what did Obi-Wan say when he gave that aforementioned lightsaber to Anakin in the first place?"This weapon is your life."
Foreshadowing / Attack of the Clones