Gen 1: Venusaur, Charizard, Blastoise, Butterfree, Beedrill, Pidgey (one of my most recent ones, I still have to evolve it), Raticate, Arbok, Pikachu (event), Raichu (event), Sandslash, Nidoking, Clefable, Golbat, Venomoth, Dugtrio, Arcanine, Golem, Rapidash (my first one, back in Leafgreen), Slowbro, Farfetch'd, Gengar, Kingler, Cubone, Marowak, Weezing, Seaking, Magikarp, Gyarados, Lapras, Ditto, Eevee, Vaporeon, Jolteon, Flareon (these were cloned from the same Eevee though back in Emerald, I didn't get multiple shiny Eevees), Omastar, Kabutops, Aerodactyl, Dragonite (in-game event)
Gen 2: Meganium, Typhlosion, Ledyba, Ledian, Crobat, Lanturn, Pichu (event), Ampharos, Bellossom, Politoed, Quagsire, Umbreon (yup, still same eevee), Girafarig, Dunsparce, Steelix, Heracross, Ursaring, Swinub (not evolving it), Remoraid, Octillery, Skarmory, Kingdra, Raikou (event), Entei (event), Suicune (event), Tyranitar, Lugia (first successful SR one)
Gen 3:
Sceptile, Cascoon, Dustox, Swellow, Pelipper, Gardevoir, Breloom, Nincada, Ninjask, Shedinja, Exploud, Electrike, Manectric, Gulpin, Swalot, Sharpedo, Wailord, Camerupt, Flygon, Cacturne, Whiscash, Armaldo, Milotic, Castform, Kecleon, Banette, Relicanth, Luvdisc, Salamence, Metagross, Regice
Gen 4:
Bidoof, Bibarel, Roserade, Skuntank, Spiritomb, Garchomp (in game event), Lumineon, Weavile, Magnezone, Leafeon, Glaceon (same eevee like the rest), Gallade, Dusknoir, Palkia (event), Dialga (event) Giratina (event)
Gen 5:
Unfezant, Gigalith, Basculin, Dwebble, Garbodor, Zoroark, Cinccino, Reuniclus, Klingklang, Fraxure, Haxorus (in game event), Braviary, Hydreigon
Gen 6:
Greninja, Gogoat, Pangoro, Meowstic, Aegislash, Aromatisse, Slurpuff, Skrelp, Dragalge, Tyrunt, Tyrantrum, Sylveon (same eevee like the rest), Dedenne, Goodra, Noivern