Listmania!
Best Thinking Puzzle + Brain Training DS Games
By an Amazon.com customer
PrismPrism
Buy new: $19.52 / Used from: $7.49
An excellent logical challenge on the harder levels. One of my favorites.
GravityGravity
Buy used from: $15.99
~*~ You have to construct objects to get the ball to hit the goal. It's a simple well-done physics puzzler.
NevesNeves
Buy new: $79.99 / Used from: $12.95
~*~ You are given a silhouette to fill with special shapes. Excellent for improving spatial visualization skills.
ExitExit
Buy new: $15.09 / Used from: $7.00
Similar to Toki Tori, with a little bit more action.
Honeycomb BeatHoneycomb Beat
Buy new: $10.36 / Used from: $7.48
~*~ Tile turning pattern game. Quite challenging on the later levels.
PolariumPolarium
Buy new: $14.11 / Used from: $2.80
~*~ A simple idea elegantly employed. It and its sequel are worth getting if you like spatial-thinking puzzles.
Polarium AdvancePolarium Advance
Buy new: $10.48 / Used from: $3.96
This is actually the SEQUEL to the DS version. I don't know why they did it that way, but this actually has three times the puzzles than the DS version and lets you change the colors.
Denki BlocksDenki Blocks
Buy new: $67.98 / Used from: $6.01
~*~ Don't be fooled by this game's cute graphics, this is the best and most challenging spatial logical reasoning puzzle game I have ever played. One of my all time favorites.
Brain VoyageBrain Voyage
Buy new: $18.64 / Used from: $11.00
~*~ Collection of mini-puzzlers, including variations of many classic thinking games.
Mechanic MasterMechanic Master
Buy new: $15.00 / Used from: $17.99
~*~ Rube Goldberg lives!
Chu Chu RocketChu Chu Rocket
Buy new: $48.98 / Used from: $1.05
Rubik's WorldRubik's World
Buy new: $21.43 / Used from: $4.95
~*~ Logical mini games plus learn how the algorithm to solve Rubiks Cube.
Steal PrincessSteal Princess
Buy new: $32.35 / Used from: $22.79
Sequential step puzzler but with major RPG elements.
Professor Layton and the Curious VillageProfessor Layton and the Curious Village
Buy new: $24.82 / Used from: $10.00
~*~ Excellent in every way. I intend to buy all eight sequels.
Professor Layton and the Diabolical BoxProfessor Layton and the Diabolical Box
Buy new: $29.82 / Used from: $26.99
ScribblenautsScribblenauts
Buy new: $18.96 / Used from: $24.29
Creativity as unbounded as any puzzle game ever made so far.
Double Sequence: The Q-Virus InvasionDouble Sequence: The Q-Virus Invasion
Buy new: $14.79 / Used from: $14.99
Has a poorly designed interface but the actual spatial logic block moving game is quite a good challenge.
MatchstickMatchstick
Buy used from: $10.69
~*~ Bare bones presentation, but if you like match puzzles it is still worth getting.
Safecracker: The Ultimate Puzzle AdventureSafecracker: The Ultimate Puzzle Adventure
Buy new: $27.99
Basically a sampling of many different types of puzzles.
ZendokuZendoku
Buy new: $13.23 / Used from: $9.99
sudoku but with non-numeric symbols
Jumble MadnessJumble Madness
Buy used from: $16.00
~*~ Nearly as good as the paper.
Picross DSPicross DS
Buy new: $74.69 / Used from: $9.90
Similar to Sudoko. Good relaxing logical reasoning challenge.
Picross 3DPicross 3D
Buy new: $39.99 / Used from: $14.99
Chessmaster: The Art of LearningChessmaster: The Art of Learning
Buy new: $139.97 / Used from: $18.00
good for beginners and intermediates plus has surprisingly good mini games.
Fritz ChessFritz Chess
better for advanced players
Mr PantsMr Pants
Buy new: $22.65 / Used from: $11.70
Brain ChallengeBrain Challenge
Buy new: $134.89 / Used from: $26.97
IMO, the best of the brain training clones. There is also an excellent Wiiware version.
Big Brain AcademyBig Brain Academy
Buy new: $44.98 / Used from: $12.95
Brain Age 2: More Training in Minutes a Day!Brain Age 2: More Training in Minutes a Day!
Buy new: $18.24 / Used from: $10.99
Flash Focus:  Vision Training in Minutes a DayFlash Focus: Vision Training in Minutes a Day
Buy new: $29.99 / Used from: $7.89
Brain AssistBrain Assist
Buy new: $17.05 / Used from: $5.50
Master Jin Jin's IQ ChallengeMaster Jin Jin's IQ Challenge
Buy new: $29.99 / Used from: $11.99
~*~ Fun mini-games with challenging riddles.
Brain Age: Train Your Brain in Minutes a Day!Brain Age: Train Your Brain in Minutes a Day!
Buy new: $18.72 / Used from: $10.81
th!nk Logic Trainerth!nk Logic Trainer
Buy new: $19.99
Not out yet. I will update this after I try it.
Mindstorm 2Mindstorm 2
Buy new: $29.99
Not out yet. I will update this after I try it.