In the queue for Mission:SPACE there's a big gravity wheel-thing that turns, and in the center is the classic EPCOT Center logo for the Horizons attraction, which was replaced by M:S. Also, in The Many Adventures of Winnie the Pooh, there's a picture in Owl's house depicting Mr. Toad handing the deed to the property over to Owl, (Mr. Toad's Wild Ride once occupied the space.) In Journey into Imagination with Figment in Epcot, there's an office door reading "Dean Finder," referring to the lost character "The Dreamfinder." In the barn that is part of the queue and ride for the Barnstormer roller coaster in Mickey's Toontown Fair, there are animatronic chickens that were once a part of the World of Motion attraction in Epcot. In Pooh's Playful Spot (Fantasyland playground on the site of old 20,000 Leagues lagoon,) there is a little silhouette of a Nautilus submarine in one of the door frames.
(I've never visited Disneyland Resort, Tokyo Disney Resort, Disneyland Resort Paris, nor Hong Kong Disneyland Resort, so don't be fooled when I pretend to know what I'm talking about. [But I'm pretty good with the information, if I do say so myself. And you can hit me all you want with Walt Disney World.])
The back area of Frontierland is loaded with nods and homages to Mine Train Thru Nature's Wonderland:
• The most obvious, Bear Country lake is still in existence with a lone mine tunnel, where the former trestle use to the span. The jumping fish are still operational, though the bears are long gone (the one that use to scratch his back on the tree was located along the River's of America for a while until recent years).
• Another tunnel, different than the one that looks over the Bear Country lake is the tunnel that leads to Cascade Peak, or rather the plot of the Cascade Peak. This tunnel is boarded up these days, and when the ride was operational, marmots would bark and pop up and down from the top of the tunnel; they are now located on the very last surviving mine train that is staged as a wreck along the Cascade Peak track. (The train, I think, is being torn out at the moment).
• The large buttes and the natural arch in front of Big Thunder ranch are remains from the Living desert area; these are NOT to be confused with the rock columns of Balancing rock canyon (which use to located where the mining equipment vignette featuring a locomotive from the movie 'Hot Lead and Cold Feet' is now).
• In Big Thunder Ranch, there is a rock ridge along the side that borders Fantasyland; that was part of the rockwork that was backdrop for the mine trains when they passed the geysers and the paint pots. It's buried in a couple feet of concrete along with the faux mine tunnel, which only the top half is exposed today.
• Rainbow Caverns is paid a tribute in the cave of the first BTMRR lift hill, as well as the 'Laughin' place scene on Splash Mountain.
• The mining town in the Big Thunder queue are the exact same buildings from Rainbow Ridge.
• The coyotes that you saw before entering Balancing Rock Canyons were
relocated to rock ledges seen before the turn before the second lift
hill on Big Thunder Mountain (the ones that go "Yipp! Yipp! Yipp!" ).
• Although guests can't access it, there is a small stretch of the old Pack Mule trail, intact and untouched.
In the second room of the Star Tours queue, look down near the top of the ramp and you will see this droid at a control panel. This is actually a redressed display case from the Adventure thru Inner Space queue:
The old Fantasyland Station for Skyway is still visible which can or not be counted as a nod to what was once there (I count it). Suffice to say, the holes in the Matterhorn were filled up when Skyway closed.
The Mark 7 Monorail's design (exterior wise) is a nod to the Mark 1 monorails (minus the bubble thing on top)
Just after the first bridge, there is a piece of wood above your head that has "Mind thy head" painted on it. This was originally in the Swiss Family Treehouse.
Some of the pots and pans in the treehouse itself (not the ones guests bang on at the bottom) are from the Swiss Family Treehouse.
At the base of the treehouse, there is a gramophone that plays the "Swisspolka" from the Swiss Family Robinson movie. There is also a teapot and teacup that look exactly like Mrs. Potts and Chip from Beauty and the Beast, but without the facial features.
On Buzz Lightyear Astor Blasters at Disneyland in the Final Battle Scene there is a sun and moon from Circle Vision. It is located up above the exit from hyperspace and is extremely difficult to see while the ride is in normal operation.