Out of the games that I've played, I would have to say that Professor Layton and the Unwound Future is my favorite title. I've been a fan of the series ever since the second game released. However, I believe the sequel is far superior. The storytelling, the musical score, the atmosphere, and the puzzles all come together to produce one of the best titles that Level 5 has ever produced. Although Diabolical Box was great as well, I still would place it, Curious Village, and the prequels behind Unwound Future.
As far as Zelda games go, I would have to say that The Wind Waker HD is my favorite. Initially when I played the game, I got frustrated with the sailing aspect. I even put the game on a long hiatus. It wasn't until maybe a year that I came back to it, and am I glad that I did! Wind Waker HD perfectly captures the thrill of exploration. Over time, sailing the vast sea eventually started to grow on me. Even though the game is lacking in dungeons, I believe the story is one of the most captivating in the series. I especially loved the final boss fight with Ganon. If you don't have it already, what is wrong with you? Pick it up at your local store for $20. You'll be glad that you did.