I would have label Emerald as my favorite. Aside from it seamlessly combining the stories of Ruby and Sapphire, Emerald added many innovations that would later become staples in the series such as Contests and The Battle Frontier. However, probably my favorite thing about Emerald was the music-oh the music. Pokemon Emerald has one of the greatest soundtracks in all of gaming.
I voted Black & White, because I'm young and I didn't play that much games. And out of all the Pokémon games I played (Diamond & Pearl, Heartgold & Soulsilver and Black & White), I liked Black & White the most.
My favorite Pokemon game is either Mystery Dungeon Red & Blue Rescue Team or Mystery Dungeon Explorers of the Sky, besides that it is either Diamond & Pearl or Yellow (I haven't played Black and White yet). Yellow only had the original 150 Pokemon (Although I'm fine with the 2nd and 3rd gen Pokemon as well), plus you could get a Venusaur, Charizard, and Blastoise without having to trade.
Mine would have to be Ruby
Ruby was the first Pokemon game I played. After awhile I got Sapphire, and I got every other game after that leading up to Platinum (never got any new pokemon games after that) and heck I even got Crystal.
But Ruby is my favorite. (Besides Deoxys, which you can't really get legit) my favorite legendary is Groudon. Mudkip is my favorite starter. I love Jirachi, Rayquaza, and Kyorge is pretty cool, but I personally like Groudon better. I just re-bought Ruby and i'm loving it so far! Now I could have bought Emerald to get the feel of both Ruby and Sapphire. But Ruby will always remain my favorite. I got my first lv. 100 in that game, and that was the first pokemon I beat.
I'm not planning on getting HeartGold/SoulSilver or Black/White or whatever. But if they remake Ruby & Sapphire for the 3DS (possibly DS) then I am for-sure buying the Ruby remake!