Topic title pretty much speaks for itself. I've separated Ruby and Sapphire from Emerald because some people might've enjoyed playing through the either of the first two games more than Emerald, considering how RS brought forth a new region, while Emerald was more akin to a director's cut.
Anyway, my favorite 3rd Generation game (and really, my favorite Pokemon game of all time after Platinum) is Emerald. Pokemon Emerald took everything that was great about Ruby and Sapphire while managing to combine their stories into a great one. I loved how Rayquaza was implemented into the story, and the war between Kyogre and Groudon. The Battle Frontier was easily the best addition, however, and really brought forth tons of replay value.
Click here to visit the "Platinum vs HGSS" thread.