Johto 100% Who can forget saving the Miltank, or crossing that huge area of water inbetween the lighthouse place and Cianwood or w/e? Not to mention, you beat the elite four and it isn't just, ok now catch some legendaries. It was REVISIT FREAKING KANTO! Awesome, can't wait for a remake.
I liked the Johto and Kanto Pokemon the best, and the GSC games were my favorite. Probably because Pokemon Crystal was my first ever video game and I didn't play the 3rd gen games because I didn't have a GBA. But even now that I have D/P I still like Johto the best.