After Bane escapes from the Resolute, Anakin angrily holds his arms behind his back, and walks away, much like Darth Vader does at the end of Star Wars: Episode V - The Empire Strikes Back (1980) after the Millennium Falcon escapes.
Admiral Yularen's line, "No! Lock them all down, hurry!" is a reference to C-3PO's line, "No! Shut them all down, hurry!" in Star Wars: Episode IV - A New Hope (1977), when R2-D2 is attempting to shut down the trash compactors aboard the Death Star.
When Mace Windu rolls under the closing door and Force-pulls his lightsaber back through it, this is a reference to Indiana Jones, where Indy makes a similar last-second grab for his whip in Raiders of the Lost Ark (1981), and for his hat in Indiana Jones and the Temple of Doom (1984).
The holographic mobile above the Gungan toddler's crib includes a Colo Clawfish and a Sando Aqua monster, both of which were seen in Star Wars: Episode I - The Phantom Menace (1999)
The 'Jedi fortune cookie' message that opens the show reads "The first step to correcting a mistake is patience."