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Examples include dual slot Pokemon and Spiritomb in DPPt and Giratina in ORAS. Please ignore Friend Safaris in the answer and don't question my curiosity.

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What are you talking about? He/she did comment.
It was an answer at first; I guess he converted it into a comment.
garatina palkia and dialga in Pokemon soulsilver
Pokémon ranger manaphy?
HGSS Dialga, Palkia, and Giratina require events, not interacting with another game. I don't think Manaphy counts because Ranger isn't a core series game.

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I talked to a few Bulbapedia editors since I asked this question. Hopefully their combined knowledge is enough to write a complete answer.
E: Surskit
DP: Caterpie, Weedle, Ekans, Sandshrew, Vulpix, Growlithe, Gengar, Pineco, Gligar, Shuckle, Teddiursa, Elekid, Magby, Lotad, Seedot, Sableye, Mawile, Zangoose, Seviper, Lunatone, Solrock, Spiritomb, Regigigas
Pt: Caterpie, Weedle, Ekans, Sandshrew, Vulpix, Growlithe, Gengar, Pineco, Shuckle, Teddiursa, Lotad, Seedot, Sableye, Mawile, Zangoose, Seviper, Lunatone, Solrock, Spiritomb, Regigigas
HGSS: Rayquaza
BW: Landorus
B2: Regice, Regigigas
W2: Registeel, Regigigas
XY: every Friend Safari Pokemon
ORAS: Regigigas, Giratina, Landorus, Kyurem
USUM: Rayquaza, Regigigas, Giratina, Landorus, Kyurem
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