Well I have a few.
For the my absolute favorite, it would be Pokemon Black. It is my favorite in the series for just about everything you could think of when liking the game. It has the perfect Pokemon formula down, along with the great Pokemon, an interesting story compared to other Pokemon games, good characters, great music. I love all the Pokemon games, but this is still my favorite.
For the traditional JRPG, it would be Golden Sun/Golden Sun: Lost Age I count them as one big game since that is how they were designed. A great combat system, good puzzles and dungeons, cool characters, amazing music, lots of great content. Can't go wrong with Golden Sun.
I'll also throw in Paper Mario Thousand Year Door. Great characters, funny writing, great locations, a good tone and story, lots of things to do. It built a world that is fun to explore in, the same could be said for the other entries on my post.