The Drowning Pit sequence. Mickey struggling to swim upwards even though he's chained up, noticeably exhaling when he can't hold his breath, and finally fainting. The air bubbles that escapes his mouth even form his famous head silhouette. Also counts as Mood Whiplash with the sign gag: "You must be THIS TALL to survive the dungeon."
Although the sign gag is Played for Laughs, Mickey's face when he sees this basically says "That's it, I am going to die."
A gag with tombstones for the trio in Pete's lair, each one with a carved skull shaped like the character's heads on top of each one.
A minor one, but during Goofy and Clarabelle's love song, a very conflicted Clarabelle (who's a villain in this special) has a chorus of imaginary hooded cows ominously floating around her and telling her not to fall in love with Goofy because they're supposed to be enemies. One of their lyrics is "You have to kill him or he'll change your mind!" Yes, that's right—Clarabelle's conscience was basically telling her to straight up murder Goofy. Fortunately, Goofy's song and Clarabelle's High-Heel–Face Turn changes their tune as well.
Strawman Has a Point: Pete is undoubtedly the villain of the film and has a low opinion of the main trio, but at the beginning of the film, he makes a valid point in saying that their shortcomings (Donald's cowardice, Goofy's dimwittedness, and Mickey's short stature) would make them unbefitting of musketeer work. If the three of them were made musketeers without going through Character Development, Donald would most likely run away in terror from any opponent he faced, Goofy would be easily outwitted, and Mickey would (probably) fail at having anyone take him seriously or defeating larger opponents due to his short size. If Pete wasn't the villain of the movie, his refusal to make the three musketeers would've been out of desire to keep them out of harm's way and/or to ensure nobody gets hurt due to their flaws.