The firing sequence of the Malevolence's ion cannon with two Battle Droids covering their eyes as the laser shoots past them is a nod to the shot of the Death Star firing in Star Wars: Episode IV - A New Hope (1977).
The look of the Clone Wars-era Y-wing bombers stems directly from the design of the original Y-wing and speculation from Episode IV Visual Effects Art Director Joe Johnston that the Rebel Alliance Y-wing was a "chopped" version of an older craft. An earlier idea of a skinned or fully faired Y-wing appeared in the Star Wars: Incredible Cross-Sections book from DK, but that design differs from the final look of the Y-wing bombers seen in this episode, which more effectively bridges the design aesthetic of the prequel and original trilogies.
The 'Jedi fortune cookie' message that opens the show reads "Easy is the path to wisdom for those not blinded by themselves". In the original script it said "Easy is the path to wisdom for those not blinded by ego."
The four-legged power droid seen in the Republic hangar is a PLNK-series droid, named after the distinctive 'plunk' sound it makes, and also after it's designer, Kilian Plunkett.
The Kaliida Medcenter was designed by Thang Le, who wanted to pay homage to both 2001: A Space Odyssey (1968) and real life space stations. When shown from the top down, the Medcenter is actually designed to resemble the Republic symbol.