I love the nods to the previous attractions!
Now, I don't really know about ones at WDW, but I know of a few at DL.
One was already mentioned in Winnie the Pooh...and it's one of my favorites.

When Innoventions was still open, if you looked on the ceiling in the "demo" areas where you first entered the building, you would eventually see some stars still affixed to the ceiling from the show "America Sings".
Also, in addition to Captain Rex in Star Tours, in the original queue area there was a conveyor carrying droid parts (I'm not sure what it's currently doing)...that was part of "Adventures Thru Inner Space"...and in the original movie the "mighty microscope" could be seen.
Also, the rocket located outside of "Redd Rockets Pizza Port" was part of either "Rocket to the Moon" and/or "Mission to Mars"...I can never remember the exact story on that one.
At the end of the Finding Nemo Subs attraction, the sea serpent from the original "Submarine Voyage" can be seen.
Those are the ones I can think of for now...I'm sure there are others I'm not aware of.
I love these sort of things...and thank you for starting this thread! I look forward to looking for some of these whenever we get back to WDW!
