For me, I liked Crystal the best. It up'ed Gold and Silver's storyline, and I loved that they added the animations to the sprites. I also enjoyed that it brought back Kanto, and added a whole storyline to that, with the whole "3 years later" ordeal.
After that, comes R/S/E mainly because of the epic music, and I just loved the Hoenn Pokémon. And the storyline is pretty good too, but it does move by quickly.
D/P/Pt come last, I hated these games. The creatures were un-original, their cries sound terrible and the plot was too thick. Too many legendaries as well! I don't need 12 of them...
Oh yea, Yellow is the best just because it is the best and no one can say otherwise. :D