I just caught this weird Pikachu.....

there are a lot of subtle differences...too many to mention but the ones I can think of are:
female venusaur has a seed on top of the flower
female wooper's antenna/ears are smaller
female Scyther/Scizor's abdomen is bigger
female Donphan's tusks are smaller...etc...etc...
If you'd like you can look at them here http://serebii.net/pokedex-sm/194.shtml

Male Gligar is slightly bigger in the tail stinger than female Gligar.

His tail waves below the line of the stats screen overlay...hers does not reach that low.