OK this isn't an exhaustive list but you can add your own that you know of but this is what I know:
When you enter the first cave / A lift it pays homage to the old Mine Train through Nature’s Wonderland.
After the snow shed to the left is the rides Hidden Mickey in the form of three gears that are stregicaly placed upside-down. Legend has it ride operators made it themselves.
To the right as you are going up B lift past the Hidden Mickey there is a genuine steam engine from long ago, now powered by and electric motor. But when it breaks down they have to order parts from the original manufacture or build it from scratch.
After you crest B lift past the Goat chewing dynamite, there is a big foot in the rockwork just as you pass under the lift before spiral butte. This was placed there because when they were testing the ride back in the day a WDI engineer was test riding the train and it derailed and he broke his toe so it’s homage to him.
As you make the turn before C lift there is a wall of, I guess the best way to describe them is telephone poles. That used to be a viewing area but a train derailed there and they decided to make sure if it derailed again it wouldn't hurt bystanders. They also added a third rail there to help it not derail.
And finally the little town at Brake Zone 4 after the Dino pond is also left over from Mine Train through Nature’s Wonderland.
This is what I can remember; if you have more feel free to post.