Transformers has several references to Chicago here and there within the physical props (where the ridefilm takes place), and of course there's the original VW Yellow Bug that was Bumblebee in the original cartoons.
In the panic room portion of the queue, General Moreshower gives out the order to initiate a protocol "Bravo Alpha Young", which abbreviated is of course, the surname of Michael Bay.
In the final room of the queue that has the safety video running, if you look up really high you'll see a light completely off. When the show building was built, the electricians forgot to wire that light since it was in such an odd, obscure area, and thus it's just languishing there never to be lit. Due to maintenance not having a way to reach it so it can be removed, I guess it's staying haha!
In ROTM there is a doll of E.T. in the treasure room. Yes, it's still there.
In Jurassic Park, there is a Barbasol can hidden on the other side of the unload platform. And of course, the infamous Mickey hat in the water by the crashed boat backstage, which at one point had "Michael" written on it for then-CEO Michael Eisner.
In Special Effects Stage, you can see props from lots of past Universal shows, like Fear Factor, the original SES and Creature.
In the Kwik-E-Mart, many of the signs and props used were former "themeing" for 7/11s across the country when they were themselves turned into Kwik-E-Marts for the promotion of "The Simpsons Movie" in 2007. (The Simpsons Ride opened in 2008)
Inside the final waiting room of The Simpsons Ride, you can spot a photo of Krusty standing with Matt Groening, the creator of the show.
That's all I have for now!
EDIT: Oh, and btw Chris I'm not sure if you've heard them but Lou Mongello has an amazing series of podcasts where he travels around Walt Disney World with Disney historian Jim Korkias and they explore all these hidden easter eggs on property (and talk about the history and significance and such), and they record it live as they go around. I'm not sure if that would be possible for you guys to do, but it would be really neat!