Around 12 minutes in, as Wat Tambor is loading "valuables" onto his ship to evacuate the planet, one of the said "valuables" is easily recognizable as the Ark of the Covenant, as seen in Raiders of the Lost Ark (1981).
Clone Commander Ponds has an Aurebesh phrase written on the back of his helmet that reads, "some guys have all the luck".
The 'Jedi fortune cookie' message that opens the show reads "Compromise is a virtue to be cultivated, not a weakness to be despised."
According to The Art of Star Wars: The Clone Wars book, designer Jackson Sze based the look of the capital city of Lessu on Minas Tirith as seen in The Lord of the Rings: The Return of the King (2003).
Twi'lek Cham Syndulla wears the same kind of chest armor as Bib Fortuna in Star Wars: Episode VI - Return of the Jedi (1983) and the same customized DL-44 blaster pistol used by Han Solo. Unlike Solo, Cham carries a second blaster pistol, an LL-30.