Puzzle games aren’t just supposed to bend our minds, but also offer unique ways to play puzzles we’ve grown to love. Some have stories, some require reflex, and some just make you think.
Professor Layton and the Unwound Future
Professor Layton brings puzzle games to life with a charming story, visuals, and deep clever puzzles. What sets it apart from the rest is the way puzzles are presented with the DS hardware and the way you think about them. Professor Layton has set the standard for puzzle games, and you don’t just have to have the quantity to make a puzzle game great.
Runner-Ups
Mario vs Donkey Kong: Mini-Land Mayhem
Puzzle Quest 2
The Undergarden
The Misadventures of P.B. Winterbottom
thebinarymessiah.com 
Yep! The fact that I forgot about this game until you made a comment proves that.