One of the signboard in the First Mission oneshot has a Principality of Zeon sign on it. It's hard to see unless you take a good look at said page.
The way the YAMA virus makes threats to send the world into a nuclear war is similar to what Skynet would do. The computer it infects also bears some resemblance to HAL
Rick Bordeau's first introduction in Romania to Jean can be seen as a homage to the Star Wars franchise. Ryoji Minagawa is an avid Star Wars fan, having watched it because it was made by George Lucas.
In "The Forest of No Return" episode, Yoshino shouts if they're in a Night of the Living Dead situation after she and Yu meet Akatsuki for the first time.