General Grievous greets Obi-Wan with "Hello there!" - A reference and taunt of the same phrase that Obi-Wan will use to Grievous in Star Wars: Episode III - Revenge of the Sith (2005) on the planet Utapau.
Anakin says to Obi-Wan that spinning is "a good trick", referring to flying. This is a direct reference to what Anakin said towards the end of Star Wars: Episode I - The Phantom Menace (1999). He also puts his own advice to good use in the opening scene of Star Wars: Episode III - Revenge of the Sith (2005).
The internal train system on the Malevolence warns its departing passengers to "Mind the gap"; this is the same message played on trains around the World.
After Anakin decides to go rescue Padmé, Plo Koon says he goes "craving adventure and excitement". This can be seen as a reference to Star Wars: Episode V - The Empire Strikes Back (1980), where Yoda says to Luke: "Adventure. Excitement. A Jedi craves not these things."
Some ideas from the original script of the episode included: Captain Panaka from Star Wars: Episode I - The Phantom Menace (1999) being captured alongside with Padmé and being brutally murdered by Grievous; a lightsaber duel between Grievous and Plo Koon on the exterior of Malevolence in space; and Jedi sneaking aboard the Malevolence by freezing themselves in carbonite to get past droid bio scans and radiation beams.