I did not watched second season of Clannad, but last time I checked, Kyou had long hair, and I havent seen much fan-art of her with short hair, since that would be stupid, since shes got a twin looking like that

Hint: Kyou After OVA.

Despite being twins, you should be able to discern the differences in their faces if you study them closely.
However, I already can tell them apart, so I'm just going to look at boobs.

Another hint, one that's more obvious and spoiler-free: EYE COLORS.

Also, Ryou wears the hair ornament on her right side, Kyou on the left.