I'm going to list evolutions in general because I can. Also, probably due to the fact that I hate most of gen 4 and can't remember them.
Milotic, Altaria, Wailord, Beautifly, Blaziken, Blissey, Houndoom, Bellossom, Ampharos, Lanturn, Typhlosion, Jolteon, Flareon, Gyarados, Starmie, Marowak, Kingler, Gengar, Cloyster, Dodrio, Dewgong, Rapidash, Weepinbell, Poliwrath, Arcanine, Primeape, Golduck, Dugtrio, Ninetales, Pidgeot, Butterfree, Charizard - all in no order
But, for more than one generation? Um. Blissey & Bellossom. Since they're the only ones I believe are cross-gens, so... :( Oh, and Azurill, the pre-evo, I love it.
Overall though, Johto produced the best new Pokemon, while Kanto brought the best evos (aside from those three.)