A couple of first-season episodes have snuck in artifacts. A senator had a cane styled after the Staff of Ra (which later served as a sort of Weapon Tombstone) and one of the treasures Wat Tambor tried to loot from Ryloth was the Ark of the Covenant. Much later at the end of the third season, a crystal skull is in the Trandoshans' trophy room.
Mace Windu loses his lightsaber on one side of a closing door and gets it back at the last moment, similar to the Indiana Jones scene with the hat.
"The Hunt for Ziro" features a dance number performed by Sy Snootles and three Twi'lek girls, that's very similar in to Wille Scott's Anything Goes from "The Temple of Doom".
It's also highly reminiscent of the 80's Droids cartoon.
In the climax of "Prisoners", Prince Lee-Char kills Riff Tamson by shooting an explosive attached to Tamson's body while he charges at the prince. Riff Tamson is a shark (or, Sharkman, that is). Also earlier, in "Water Wars", the music played when Tamson was seen swimming through the battle field, surrouned by the corpses of Mon Cala soldiers, eerily resamles the infamous Jaws main theme.
The relationship between Morley and Darth Maul in "Brothers" resembles the one between Gollum and Shelob.
The scene in which Obi-Wan finds the Dagger of Mortis is a reference to the scene of Wagner'sThe Ring of the Nibelung, when Siegfried passed through a ring of fire to find Brünhilde.
The scene when Father regains consciousness is similar to the last scene of Avatar.
An other Avatar reference from Friends and Enemies: after he was KO-ed by Bane and Hardeen, Ahsoka crounched protectively over an unconscious Anakin much the same way Neytiri crounched over Sully's avatar-body after the battle with Quaritch.
The episode also features Kiera Swan, a female weaquay pirate-turned bounty hunter, and two-time winner of the Obsidian Sphere. Kiera for Keira Knightley, Swan for Knightley's Star-Making Role of Elizabeth Swann, a female pirate, and Obsidian Sphere for Black Pearl, reads Pirates of the Caribbean.
In "The Lawless" some memberes of the faction of Death Watch loyal to Maul, had a black hand on their helmet. This migh refer to Saruman's orc army from Lord of the Rings, who wore the mark of the white hand, since Maul was very in a similar postion to Saruman.
In "Fugitive" upon being told to try act normal, so he and Fives can pass by a pair of kaminoians without drawing attention to them, AZ-3 mimicked the "annoying Kurriboh-speech" from Yu-Gi-Oh! The Abridged Series.
In "The Gungan General", the pirate who has Dooku, Anakin, and Obi-Wan captive, tells them that he'd hate to kill them, "you seem like decent fellows".
In the movie Anakin quoted Qui-Gon's "Nothing happens by accident." to reassure Ahsoka that she doesn't have to prove herself worthy of being his Padawan.
Also in the movie, Dooku and Ventress replicate the infamous "We shall double our effort." part of Vader's conversation with the commader of the second Death Star, at the beggining of Return of the Jedi.
The Story Arc also introduced an early version of the original trilogy Y-Wing bomber.
The Delta-7 Jedi fighter Anakin gave to Plo Koon in "Shadow of Malevolence" is the same one Plo Koon was flying when he was shot down in Revenge of the Sith, during the execution of Order 66.
In "Destroy Malevolence" Grievous jumps down behind Obi-Wan and greets him with a "Hello, there." Obi-Wan does the same thing to Grievous in Revenge of the Sith, in a retroactive Ironic Echo.
In "Cloak of Darkness"
After a furious lightsaber-exchange, Luminara and Ventress Force-pushed each other simultaneously, much like how Anakin and Obi-Wan did during their duel in Revenge of the Sith.
Later in the episode Ahsoka also said "We'll take her [Ventress] together". Obi-Wan used this line (with proper pronoun of course) prior to him and Anakin confronting Dooku earlier in the same movie.
In The Phantom Menace, Anakin originally confuses Padme with "an angel", the most beautiful creatures in the universe that pilots say live on the moons of Iego. Lo and behold, Anakin and Obi-Wan go to Iego and meet an angel, and the Separatists were testing a prototype of the Death Star superlaser on Iego's moons.
In "Dooku Captured" Obi-Wan quips "You're not the prisoners I'm looking for.", when he accidentally opens the wrong cell, while searching for the one holding Anakin.
In "Storm over Ryloth" Ahsoka used Marg Sabl maneuver, on a droid commander to devastating effect. It's the same maneuver Grand Admiral Thrawn used on an Elomin commander's taskforce.
In "Hostage Crisis" Anakin tried to prove his love for Padme by giving his lightsaber to her, with the following quote:
In "Cargo of Doom" Captain Rex made it clear, if it was not already, that clones / stormtroopers hitting their heads on things is genetic.
In "Landing At Point Rain"
Boil had Numa's (the little Twi'lek girl he met in Innocents of Ryloth) face painted on his helmet.
Obi-Wan and Ki-Adi discussed that it's hard to believe they have to battle on Geonosis once again. Later in the episode Obi-Wan also told Cody about how he was tied to a column, and had to fight several monsters.
In episode eight of season two, "Brain Invaders," Ahsoka is eating dinner and holds her fork in a Reverse Grip, they same way she always holds her lightsaber when she ignites the blade.
The large scar and cybernetic eye across Commander Wollfe's face in "Grievous Intrigue" was not present during "Rising Malevolence". That was because in the comics, Asajj Ventress slashed his face, in an attempt to retreat from a disappointing battle on Khorm.
In "Voyage of Temptation" Satine chewed out Obi-Wan for his tendency to speak in half-truths:
Also, Anakin noted that usually small ships don't have cloaking devices. This, unlike most the examples on the page, however served a purpose beyond being an eastern egg: when the imperials lost the signal of the Millenium Falcon in The Empire Strikes Back, Captain Needa stated that no ship that small can have a cloaking device. By having Anakin acknowledge how unusual the episode's cloakedship is, helped keeping the continuity together.
In the 1x06 episode Downfall of a Droid, Anakin told Ahsoka, that first hand experience is the best teacher. She tried to convince Anakin to let her go with him, by recounting it to him.
Bannamu's picture from 2x11 Lightsaber Lost appeared in the library scene, when Ahsoka was looking over the profiles of various criminals.
Ahsoka and Padmé playing dejarik, a chess-type board game. Also Padmé recounting how insecure she felt early on during her reign as Queen, before she Took a Level in Badass
When Padmé's ship arrives at Alderaan, Leia's theme is played.
The Alderaan soldiers had a helmet shaped like the helmet of the rebel soldiers in A New Hope.
In her speech at the conference, Padmé recounted the events of the invasion of Naboo, including the death of Qui-Gon Jinn.
After Ahsoka foiled her second attempt on Padmé's life, Aurra Sing recognised her as the "brat who left her for dead" in Leathal Trackdown, and explained that she survived, because Hondo Ohnaka rescued her.
The interrogator droid from "Evil Plans" is the same type as the one seen in Jabba's palace in Return of the Jedi
In "Witches in the Mist", after Savage Opress failed to complete a training exercise, he says that it's impossible, just like Luke told Yoda when he tried to lift his X-Wing from a swamp. This further contrasted by their master's reaction: while Yoda gave Luke an speech that helps him to understand the Force a little better and then lifted the X-Wing to prove that it was possible, Dooku just fries Opress with Force Lightning for not trying hard enoughnote though, to Dooku's credit, Opress then successfully completes the exercise.
Obi-Wan confused Savage for Darth Maul on the security footage.
When confronting Savage for the second time, Obi-Wan and Anakin had a very similar exchange to the one they had in Revenge of the Sith prior to their duel with Dooku:
During Anakin's and Ahsoka's duel in "Altar of Mortis", Anakin disarmed Ahsoka the same way Vader disarmed Luke early on in their duel in The Empire Strikes Back.
In Ghosts of Mortis, Anakin turns to the Dark Side to stop the Clone Wars, bring peace to the galaxy, and protect his loved ones, even if he has to kill all the Jedi to do so. [[Exactly]] what happened in Revenge of the Sith.
Fives *examining the carbon freezer*: Are we sure this thing is safe? I don't wanna end up a wall decoration
Anakin's uncharacteristic overprotectiveness towards Ahsoka isn't all that surprising once you remember what happened to her in "Altar of Mortis", two episodes earlier.
After Echo got a new Phase II armor, for being promoted to an ARC-trooper, he painted Rex's handprint on it, which Rex put on his original, "shinny" armor using a Rishi eel's blood, way back in 1x05 "Rookies". Similarly, Fives painted a stylized Rishi eel on his own helmet, as a reminder of their team mate Cutup, who was eaten by one of the eels.
In "Padawan Lost," Anakin tries to contact Ahsoka via her comm unit, which has been taken away from her. His one-sided conversation sounds suspiciously familiar to Luke's plea to Threepio for help out of the trash compactor in Episode IV. And here "familiar," means "identical."
The Trandoshan trophy room in the season 3 finale has an old style Mandalorian helmet as seen in the Knights of the Old Republic video game series.
In "Plan of Dissent", Fives replicates Han Solo's panicked conversation with a Death Star officer from Episode IV when their General Krell tries to figure out why the alarms are going off in the fighter hanger.
In the final episode of the Umbara arc, "Carnage of Krell," Dogma is warned to avoid stepping on one of the vines lying on the ground, with another clone pointing out that it is actually a tentacle for a vicious carnivorous creature and that he saw Hardcase attacked by one just like it. That happened in the first episode of arc, "Darkness on Umbara."
When Captain Rex leads a squad to attempt to arrest Krell, the entire sequence and the nature of their actions are strongly reminiscent of both Order 66 and Mace Windu's attempt to arrest Palpatine. Their target even says "It's treason, then" before tearing into his would-be captors, just as Palpatine did before tearing into his would-be captors.
In "Kidnapped" Obi-Wan asked Ahsoka if Anakin told her about his past. She replied, that he only told her, that he wouldn't talk about it. This refered to the movie, when she and Anakin were walking through the desert on Tattooine, trying to return Rotta to Jabba's palace.
The "Slaves of the Republic" slave arena scene starts as an excellent Call Forward to the start of the Sarlacc scene of Return of the Jedi - Anakin getting the eye contact from everyone, saluting, and R2-D2 shooting his lightsaber (except also with Obi-Wan's and Ahsoka's).
In "Escape from Kadavo" the death scene of the zygerian queen Miraj Scintel is a shout out to Anakin/Vader's death scene in Return of the Jedi. Miraj even quotes Anakin's "You were right."
In "Crisis On Naboo", Anakin and Palpatine enter a dining room where Dooku happened to be waiting for them ala The Empire Strikes Back which ironically has Anakin as Darth Vader doing this to Han, Leia, Chewie, and Lando.
Remember that Defoliator gun the Separatists were testing in "Defenders Of Peace"? Grievous uses one against the Nightsisters in "Massacre".
Darth Maul's design (elongated horns, shirtless, circlet around the neck, cybernetic lower body) seems to be a homage to his appearance in the non-canon comic "Old Wounds". Once he switches to his second pair of cybernetic legs, he actually becomes nearly identical to that design: only his horns were returned to their normal length.
Also, the way he draws his lightsaber just before the Raydonia massacre is just like when Anakin slaughters younglings in Revenge of the Sith.
In "Revival" Obi-Wan chews out Maul and Savage for partnering with pirates, saying "How the mighty Sith have fallen.". He used this exact line in "Dooku Captured", when he snarked at Dooku, who at the time was the prisoner of the exact same pirate gang.
The Mon Calamari arc that starts off the season is basically an expanded version of a similar underwater battle sequence on the same planet in Star Wars: Clone Wars (which was only a few minutes long), including Kit Fisto shirtless throughout.
R2-D2 and C-3PO's adventures in a couple of episodes recall the short series in the 80's staring them, Star Wars: Droids. In some ways, it reconciles the Continuity Snarl by showing them getting involved with other adventures even while a part of the big mythology stories.
In "War on Two Fronts" Ahsoka and Lux discussed their adventure on Carlac from "A Friend in Need"
The Opening Narration of "The Gathering" had a brief flashback showing Plo Koon meeting and taking Ahsoka to the Order, when she was just a toddler. This was mentioned for the first -and until then only- time in Plo's debut episode "Rising Malevolence", the second episode of Season 1.
"Sabotage" opens with a Jedi Master-Apprentice duo entering a battle with two Eta-2 Actis Jedi Interceptors, a rocket being shot at them, which missed and exploded in front of them, throwing a swarm of buzz droids on one of the ships, the droids proceeded to dismantle it, and the apprentice had to save the master. Except unlike in Revenge of the Sith, here Anakin was the one who needed to be saved by Ahsoka.
The gunship that picked up Anakin and Ahsoka after their crash is the "Lucky Lekku" with a paintjob of a blue-skinned twi'lek girl in clone trooper armor. It's the same gunship that dropped them off in the movie during the Battle of Teth.
In The Jedi Who Knew Too Much Ahsoka and Barriss recall when they were stuck inside a tank under the rubble in Weapons Factory.
Also while the fact that Rex seriously considered it possible for Ahsoka to have killed three clones, might sound strange at first, but when you remember what General Krell put him through, it's understandable that he wasn't willing to take risks.
The ending of the episode is highly reminiscent to the climax of The Empire Strikes Back, with Anakin/Vader trying to convince someone close to him to go with him, and that someone throwing themselves into the deep.
In the war-meeting scene, Obi-Wan mentions the Anoat system, where most of The Empire Strikes Back took place, as well as Saleucami, where the Season 2 episodes "Grievous Intrigue" and "The Deserter" took place.
To Catch a Jedi takes place almost entirely in the Coruscant underworld. Although it's not stated outright the streets Ahsoka is first seen strolling, look suspiciously similar to the ones shown in the trailer and on concept-arts of the canceled video game Level 1313. Rex later indirectly confirms the location, by identifying Level 1312, as the level where Ahsoka escaped to next.
The Wrong Jedi:
Anakin arriving to the trial with the proof of Ahsoka's innocence in literaly the last moment, is a throwback to the Movie, when he and Jabba's men were about to start a fight, and Ahsoka arrived just in time with Rotta, and proved Anakin's innocence.
Anakin disarmed Barriss by catching one of her wrists with his cybernetic hand, and squeezing it until she dropped her lightsaber from the pain, just like he did with Ventress during their duel on Yavin IV, in Star Wars: Clone Wars. For added irony, it's probably that exact same lightsaber.
The ending of the episode gives a nice contrast to "Wookie Hunt": during both arcs, Ahsoka had been separeted from Anakin, and then they got reunited, thanks to the aid of unexpected allies. "Wookie Hunt" ends with Anakin and Ahsoka walking back to the Temple side-by-side, with Yoda smiling proudly, "The Wrong Jedi" ends with Ahsoka leaving the Temple and Anakin, with Yoda casting his eyes down in shame. Both scenes took place during sutset.
Also the scene of Ahsoka disappearing from view as she walks down the stairs in front of the Temple's main gate, is mirroring the scene◊ of Vader appearing as he marches up on them, leading the 501st during Order 66.
In "The Disappeared Part 2" as Jar Jar and Mace entered the city where the Franglaw Cult had taken Queen Julia, Jar Jar mentioned that he has a "creeping feeling", to which Windu responded with "Do not center on your anxieties.", much like Qui-Gon did, when Obi-Wan stated that he had a bad feeling about the Trade Federation blockade at the beggining of The Phantom Menace.
The Season 6 Yoda arc features several to the original trilogy, including a trip to Dagobah's Dark Side Cave and Yoda being told "There is another Skywalker" near the end.
In "Voices" Yoda sees a vision of multiple possible futures, including some that came true in Revenge of the Sith. These includes Kit Fisto and Saessee Tiin cut down, and Windu electrocuted by Sidious. Another vision shows one of the deleted scenes of Shaak Ti being stabbed in the back by a blue lightsaber, although whether this was refering to the scene with Grievous, or the one with the newly turned Vader is ambigious.
In "Sacrifice" Yoda sees a vision of him and Anakin confronting Sidious and Dooku. In this vision, Anakin kills Dooku the same way, he eventually killed the Count: by decapiating him, using the Dooku's and his own lightsaber in a scizzor-formation. Yoda's confrontation with Sidious also includes Yoda holding Sidious's Force-lightning with his palms, until the concentrated energy blasts them apart.
In "The Unknown", the technique taught to the rebels in "A War On Two Fronts" is used to disable several destroyer droids.
Ky Narec and Dooku were both Ventress' masters and they're both voiced by Corey Burton.
In "Deception" Cad Bane mentioned that "any imbacile can kill a Jedi with a loosy sniper blast". In Ventress' Troubled Backstory Flashback in Season 3 Corey Burton voiced Jedi Ky Narec, who was killed by a pirate sniper.
In Ghosts of Mortis the Son mentions, that while the Father still has control over the realm, he'll be able to draw there any ship soon. Guess what was the most over the top feat Starkiller, another Star Wars character voiced by Sam Witwer, ever pulled?
In "Brothers", Darth Maul says the phrase "The chains, the chains are the easy part. It's what goes on in here that's hard." The same line was spoken by the disguised Son to Ahsoka in "Altar of Mortis", after she was captured.
A double dose: in the Season 3 Citadel-trilogy Stephen Stanton voiced Captain Tarkin, who was on the run from a Separatist prison, chased by the prison warden Osi Sobeck, a phindian, voiced by James Arnold Taylor. Aiding Tarkin in the escape was Obi-Wan Kenobi, also voiced by James Arnold Taylor. Almost exactly a season later in the Deception-arc, Stephen Stanton voiced Moralo Eval, a phindian on the run from a Republic prison, aided (and secretly thwarted) by Rako Hardeen, who was also voiced by James Arnold Taylor.
In a rather ironic twist Mark Hamill played Darth Bane in the final episode of the series "Sacrifice". While Darth Bane was a Sith, he carries a few key similarities to Luke Skywalker: both of them are immensely powerful Force-users, who hadn't been trained in the ways of the Force, until they were in their twenties. Like Luke, Bane was the last Sith to be trained by the masters of the old ways, and both of them recreated their own respective Orders.
It's hardly surprising that Rush Clovis was able to carry out the Banking Clan sting operation. After all, he's aprofessional thief.