Edit: Another difference is the region takes place, HeartGold and SoulSilver take place in Johto and Kanto, Diamond, Pearl, Platinum take place in Sinnoh, and Black and White take place in Unova.
Pokemon HeartGold Version and Pokemon SoulSilver Version: In HeartGold, Ho-Oh is catchable earlier than Lugia, Ho-Oh's at level 45, Lugia's at level 70, this is opposite for SoulSilver
Pokemon Diamond, Pearl, Platinum: Dialga's catchable in Diamond and Palkia's catchable in Pearl, you can get Giritina at Origin Forme and BOTH Dialga and Palkia in Platinum, Platinum also has added features and added story elements from Diamond and Pearl.
Pokemon Black and White (to come out this March!): Black Version has Black City and the legendary Pokemon Reshiram, Pokemon White has White Forest and the legendary Pokemon Zekrom.
Pokemon Ranger: It's a different kind of Pokemon game, you're not a trainer, but you're a Pokemon Ranger who tries to build "friendship" with Pokemon
Pokemon Trozei (or something like that): A Pokemon game in which I don't know what you do in.
*For all the Pokemon (insert color) Version kind of games, the big difference is what kind of Pokemon apear and how often they appear, for more information, you can go to www.serebii.net and check out the version exclusive Pokemon, and more*
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