Tie between Sapphire and Leaf Green. Emerald's overrated *shot*

. And besides, I don't have it.
I like Sapphire because, well, I don't have Ruby, either. Plus, as someone else said, R/S introduced new Pokemon, natures, contests, etc. into the Pokemon universe. And I liked LG because I don't have FR, but still. FR/LG introduced Kanto Pokemon to the Advanced Gen. The Sevii Islands, though rushed and tacked on, were interesting.
Colosseum comes in a close second, though, with its darker, more mature storyline. The Shadow Pokemon concept was an excellent idea IMO.