They both have a 2 stage evolution and version exclusives.
While they are almost the same, they are classified as two separate Pokémon and their evolutions are counterparts being Male or female only.
Clefairy and Jigglypuff
They evolve with the Fire Stone and are version exclusives.
They have a 2 stage evolution line and evolve at Level 23. Version exclusives. With Meowth being exclusive to Red and Mankey being Exclusive to Blue
They are Poison-types that represent pollution.
They have a 2 stage evolution line and evolve with the Water Stone.
Hitmonlee and Hitmonchan
Until it was revealed that they had a common pre-evolved form and another alternative evolution, they were considered counterparts.
Electabuzz and Magmar
Version exclusives. When pre-evolved forms for Jynx, Magmar and Electabuzz were released, the three could have been considered a trio of counterparts until Electivire and Magmortar were released, removing Jynx and Smoochum from the picture.
They are the first fossil Pokémon ever introduced.
The two legendary Pokémon have similar attacks, abilities and appearances as well as the back-story of Mewtwo being a clone of Mew.
Murkrow and Misdreavus
Both are verision exclusive (with Ledyba in Silver and SoulSilver and Spinarak in Gold and HeartGold), have a two-part evolution stage, and are dual types when evolved.
Both resemble cows and can only be one gender. They are one of the less commonly acknowledged counterparts but often appear next to each other in Region Pokédexes.
Generation II's eeveelutions that evolve depending on the time of the day.
Both evolve with a Metal Coat.
Version exclusives found in Johto.
Defensive flying Pokémon, Same base stats total, same HP, same Speed and Atk/Special atk Def/Special Def corretaled defense stats. Skarmory being the physical one while Mantine is the special oriented one.
These legendary version mascots are counterparts, each appear in only one out of HeartGold and SoulSilver (until you complete the main story) and both are leaders of Legendary Trios (Lugia=Articuno, Zapdos, Moltres and Ho-Oh=Raikou, Entei and Suicune).
Both are Grass-types, version exclusives and evolve under the same conditions (to get to their first stage, they need to level up to level 14 and to their final stage, they need to have a type of stone used on them).
Version exclusives that have no evolutions.
They both evolve from Nincada and represent life & death.
Both are Firefly Pokémon and can only be one gender.
The first example of counterparts that don't very many aesthetic similarities or have some kind of friendship. In fact they hate each other and fight all the time as seen by their claw marks on each other. Both have similar markings and are version exclusive.
They are both genderless, both the same type, both version exclusive and represent the sun and moon, which are opposites.
Both evolve from Clamperl and are traded with a Deep Sea held item.
Another example of version and gender exclusives.
Version exclusive version mascots which represent the land and the sea. Another example of a red and blue Counter-part.
Although both evolve from Kirlia, they are both very gender orientated, Gardevoir being feminine and Gallade being masculine.
Fossil Pokémon that are version exclusive and have a two-part evolutionary stage.
Both version exclusive (Stunky in Diamond and Glameow in Pearl) and both are used by Team Galactic's Jupiter and Mars respectively. They are also both a two stage evolution. Both Pokémon and their evolutions are unavailable in Platinum.
Both are version exclusive and evolve in the same way.
Version mascots for Diamond and Pearl control Time and Space which are often used together.
Both are related to the moon, Darkrai causes bad dreams and Cresselia cures them.
They both represent the sea and they are parent and child that cannot evolve.
Both are Fighting-type and look similar as if wearing a judo uniform with a black belt.
Both Pokémon of a 3-stage evolution.
Both are Psychic-types in a 3 stage evolution. Version exclusives.
Karrablast and Shelmet
These Pokémon can only evolve when traded with each other.
A male and female counterpart pair who are based on American settlers and native Americans. Version exclusives.
These are rivals like Seviper and Zangoose but are NOT version exclusive.
The ultimate counterparts represent Yin and Yang. Version exclusives.