Hard to say really, for sentimental reasons id say my favourite is blue because it was in the first set (and my personal first, Blastiose rocks!) though Yellow is close because of the Anime references.
As for best game I cant say as each generation improves on the one before and the directer cut versions even more so. I don't own White/Black yet so I cant judge them. I think ill still say Blue because it had the original story and a ton of features that were way ahead of its time for a classic gameboy game even with slight future connectivity in that it could still work with G/S/C to an extent and dont forget the rare candy cheat/Missingno appearance.
As for best game I cant say as each generation improves on the one before and the directer cut versions even more so. I don't own White/Black yet so I cant judge them. I think ill still say Blue because it had the original story and a ton of features that were way ahead of its time for a classic gameboy game even with slight future connectivity in that it could still work with G/S/C to an extent and dont forget the rare candy cheat/Missingno appearance.