Wait, I just thought of some more. There's the widely known one of Princess Daisy having a third eye located under her hair on her trophy in Super Smash Bros. Melee.
Also, Blanca, the weird cat without a face in the Animal Crossing series, wears a dress, but has the voice and the name highlight color of a male character.
Edit: Actually, here's another one that I just found out about maybe a day or two ago. Apparently, the Final Fantasy X and Final Fantasy 7 series share a plot related connection and therefore may exist in the same universe. Really far out there, but I kind of found it really crazy.
Also, Blanca, the weird cat without a face in the Animal Crossing series, wears a dress, but has the voice and the name highlight color of a male character.
Edit: Actually, here's another one that I just found out about maybe a day or two ago. Apparently, the Final Fantasy X and Final Fantasy 7 series share a plot related connection and therefore may exist in the same universe. Really far out there, but I kind of found it really crazy.