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I've rarely paid attention to them past the first generation, so I can't really say anything for GenII-III-IV pokemon, but from the first games, Electabuzz's was always my favorite with how it interrupted the music just to make its little sound byte. Articuno's and Porygon's/Victreebel's stick out in my mind as well
I can't pick my favorite cry, since I can't remember them all off the top of my head, but I do know that Togekiss' cry is really quite different and unique. It makes a really cool sound. If you haven't heard it, you should! ^^
Probably Eevee's! You should listen to it slowed down, it sounds weird! o.o
And second is Jigglypuff, Pikachu, Charizard, Ho-oh, Lugia, Dragonite, Tyranitar, Metagross, Rayquaza, Palkia, and Darkrai!