In The Stinger to Yoshi's New Island, Mr. Pipe's revealed to be Adult Mario in disguise. While the adult Bowser and the modern-day Kamek time traveled to the past to Set Wrong What Once Went Right, Mario, in turn, was making sure the timeline went exactly as it happened by helping Yoshi and his baby counterpart with their tasks disguised so that they won't recognize him.
World 2-3 in the original, "What's Gusty Taste Like?", does some clever foreshadowing as to what to expect in 2-4 and 2-8. Gusty itself is a ghost. The boss of 2-4 is Bigger Boo, who is a giant ghost. The boss of 2-8 is Roger, who is the titular Potted Ghost owning the castle.
In Super Mario World, Mario rescues the Yoshis as he goes to rescue Peach. In this game, the Yoshis are aiding Mario to help him reunite with Luigi. They helped him in his time of need as a baby, so now as an adult, he's helping them in theirs.
The fight against Prince Froggy in the original. It seems like quite the humorous battle...that is, until the end, where you slide straight out of Froggy. Of course, there's the obvious. Froggy craps out Yellow Yoshi. Sure, it doesn't seem bad from our point of view, but imagine what Yellow went through. The look on his face as he's freed from Froggy's stomach says it all...
That's not even considering the fact that you destroyed the uvula and ruptured the organs of a frog, which leaves said frog writhing upside-down in absolute agony (if he didn't die).