My favorite...hm hard to decide.
I'll list in order.
Soul Silver I spent the most time on, Johto region + Kanto are my favorites and it was a spectacular remake. There was pretty much endless things to do. Years back, I ended up getting an official guide and it had daily things to do so I played A LOT. Plus the Pokewalker kept my interest for an even longer time. I'd really enjoy playing it again but I don't want to reset my SS, too much I worked on. Might get Heartgold someday.
Diamond was also one of my favorites, it was one of the first DS games I got. The region was awesome, the story, the new Pokemon. The music for the game is my favorite of all the games to this day.
Last but not least is Crystal. Played it 2-3 times, my first Pokemon RPG (I played only spin off games like on n64 and gamecube before that) It's a classic, my favorite region ever and has all my favorite Pokemon.