Every girl wears white knee-highs except for Monika, who wears black thigh-highs.
Every girl except Monika wears white and blue shoes, but Monika's are white and pink.
Furthermore on these two points, Monika is positioned so close on the Title Screen that her legs up to the black thigh-highs don't even make it into the frame and cannot be seen at all, hiding her differences at first. This could be a form of foreshadowing.
Every girls' name except Monika's ends with an "i" and is explicitly the rōmaji anglicization of transcriptions originating in the Japanese language.
Every girls' sprites except one of Monika's have them facing slightly side-on. Monika's primarily used sprite has her looking directly frontward at the protagonist.
Monika is the only girl to never be shown outside of school or in a casual outfit. She later states that she knows this and is jealous of the other girls for having them, as well as wishing she could have "worn some cute clothes for you."