The only third generation game I ever owned myself was Ruby, although I got to play Emerald through friends and such, and I can definitely say that I prefer that over any of the others, which it seem most people agree with me on. I mean, just like most other generations, there isn't many seperate features to distinguish Ruby and Sapphire from each other, other than how they had different version exclusive legendaries, and how Sapphire had Team Aqua as the evil organization, and Ruby had Team Magma. If those two were the only options, I bet a lot of the answers would be biased.
Emerald, however, took a leap forward from the two, with the implemention of much prettier tiles, a slightly altered story-line, and the Battle Frontier. And while it's still very similar to Ruby and Sapphire, I felt that the game experience was better than what I'd experienced with Ruby.