I'll list favorite to least and explain why:
1) Johto. The nostalgia from this place is amazing. Loved the Japanese-style cities like Ecruteak (which was even more apparent in the remakes) and the music was just awesome, especially Violet/Olivine City, Silver's theme, and Lance/Red theme.
2) Hoenn. While I like Gen III the least overall, I thought Hoenn was very creatively designed. The music's instrumentation was bad (more of the GBA's fault) and the water routes were so so so annoying, but the cities were very well designed, especially Fortree and Sootopolis.
3) Unova. Loving the advanced technology and the introduction of changing seasons. The music hasn't stood out to me yet, but I've only had White for a week or so, so I'm still waiting to change my mind. Castelia City is awesome, it's like NYC while Saffron, Goldenrod, etc. are like "small big cities," if you know what I mean. The many bridges and towers also intrigue me.
4) Kanto. I love Gen I, but Kanto doesn't have too many distinctive characteristics since it debuted on the GameBoy. The routes look very similar and the cities don't have too many landmarks. The music is very good though, especially the Trainer battle song, Game Corner, and the Surf tune.
5) Sinnoh. I have always thought that Sinnoh is downright dull. Nothing ever really stood out to me except for Snowpoint and Floaroma. The music is average, my favorites being Floaroma, Eterna Forest, and the three lakes' theme.