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Ruby was the first Gen III game I owned, but I enjoyed Emerald the most. Just liked the new features and that you could get both Groudon and Kyogre. :3
My Rock Head, Adamant Aggron. I got it in Wonder Trade as a Lairon, after I beat the E4 and after I became Grand Duke, it was still my first Pokémon to reach level 100. And it's so satisfying to see it wreck entire teams with Head Smash. :3
It's impossible for me to just pick one.
My favorites are (in no particular order) Palkia, Luxray, Drapion, Porygon-Z and Floatzel.
I love their designs and they've all been very useful when I've used them in battles.