Caterpie Family/Weedle Family
Nidoran Family (Male/Female)
Pidgey Family/Sparrow FAmily
Abra/Machop Family (Brains Versus Brawn)
Hitmonlee/Hitmonchan/Hitmontop
Mew/Mewtwo
Articuno/Zapdos/Moltres
Eeveelutions
Ledian/Ariados (debatable, but this whole thing is pretty shaky anyway)
Raikou/Entei/Suicune
Lugia/Ho-oh
Darkrai/Cresselia
Wurmple's split family
Ludicolo/Shiftry Family
Plusle/Minun
Volbeat/Illumise
Zangoose/Seviper
Lunatone/Solrock
Kabutops/Omastar
Armaldo/Cradily
Huntail/Gorebyss
Regirock/ice/steel
Kyogre/Groudon
Lati@s
Bastiodon/Rampardos
Gastrodon (one Pokemon, but still multiple forms)
Uxie/Azelf/Mesprit
Dialga/Palkia
simisage/sear/pour
Sawk/Throh
Arhceops/Carracosta
Heatmor/Durant
Zekrom/Reshiram
Genie Trio
Musketeers
There are also the version exclusive Pokemon you could argue for, some of which are included in the list. There are a few more you could probably argue, but these are the ones I saw from the pokedex.