Updating for Gen 8! (Jan 7, 2021)
Obviously, Gen 1 Pokemon didn't have breeding; I'm just sorting this list by the generation the Pokemon was made.
Gen 1
Nidorina
Nidoqueen
Gen 2
Pichu
Cleffa
Igglybuff
Togepi
Tyrogue
Smoochum
Elekid
Magby
Gen 3
Azurill
Wynaut
Latias
Latios
Gen 4
Budew
Chingling
Bonsly
Mime. jr
Happiny
Munchlax
Riolu
Mantyke
Cresselia
Heatran
Gen 5
Tornadus
Thundurus
Landorus
Gen 6
Ash-Greninja
Cosplay Pikachu
Gen 7
None, unless you want to count that Lunala and Solgaleo are female/male, but they aren't in-game.
Gen 8
Toxel
Dracozolt
Arctozolt
Dracovish
Arctovish
Kubfu
Urshifu
... And I'm pretty sure that's it!
Sources: This and This
