Elite Beat Agents is a blast. It comes close to the best $5 I ever spent. Only reason I didn't recommend it is because it is a rhythm game and I didn't know if you'd be interested.
Professor Layton is probably the best puzzle game I've played too. I wrote a review on it before staff got banned from writing reviews. I'll post it below because I was quite proud of it cause I'm not much of a writer
A brilliantly entertaining puzzle game which has a compelling story, classic puzzles, and catchy tunes that will keep you entertained for hours. A must own for any puzzle fan.
Professor Layton and the curious village starts off with a letter which invites you to the curious village of St. Mystere. The baron has died and you have been requested to solve the riddle of the Golden Apple. Everywhere you go there is a new mystery to be solved in St. Mystere which has many secrets hidden within its walls. You play as Professor Layton and his assistant Luke as you try to solve the mysteries posed to you along the way.
The village inhabitants are infatuated with puzzles and wherever you travel people will ask you to solve their puzzle. Some people will offer hints and clues to the mysteries of St. Mystere if you solve their puzzle, while others just ask puzzles because they love them. The storyline is linear as you can only go to new sections of town when allowed, but it doesn't feel restrictive as you can solve most puzzles whenever you want. I don't wish to say much as the storyline is gripping and I wouldn't want to give away key plot points. Also, some puzzles require you to complete them before progressing with the storyline, while others are there purely for your enjoyment.
Puzzles vary in difficulty from easy to mindbogglingly tough. The harder the puzzle the more Picarats the puzzle is worth. If you give a wrong answer to a puzzle though you will get less Picarats for solving it. If you get stuck you can use hint coins, which can be found throughout the village, to give you up to 3 separate hints. Don't worry about missing puzzles or leaving them till later though, as any that are missed go to granny's house where you can solve them whenever you wish.
There are various extras like picture peices and furniture which provide a small diversion from the main story. Finding all of these and putting them where they belong will unlock extra puzzles that are more challenging.
The game is completely controlled using the stylus for exploring the village and solving the puzzles. The controls are simple yet brilliant as they allow you complete and easy control and you never wish for another input method. Some puzzles have you draw on the screen or move pieces around, while others have you select an object or enter a value on a second screen.
The graphics are all 2D, but they are beautifully done. Various first and 3rd person views are used throughout the village. Though the garphics are simple, they are charming and only add to the game. FMVs are used to aid in the story telling at various points, and they also provide full voice acting. The voice acting fits each character perfectly. There is also voice acting when they let you know if you solved a puzzle correctly or not, but sadly, other than that it is restricted to the FMVs.
The music, while not epic, is very fitting and memorable. The music fits both the charming and mysterious aspects of the game. The music loops often, but it is not intrusive and you will find yourself happily humming along with the tunes as they are very memorable.
There are 135 puzzles in the main game, and 15 extra puzzles that you can unlock by meeting certain conditions. Also, there are 24 weekly downloadable puzzles still available, however the weekly updates have ended and I don't expect any more. Overall the game should last around 10-15 hours of gameplay depending on how familiar you are with some of the tougher classic puzzles. I personally managed to beat every puzzle in ~12 hours. Once you beat the game though there is little replay value unless you forget puzzles very easily.
Overall this is a must have title for any puzzle lover that owns a DS.