Listmania!
Best Thinking Puzzle + Brain Training DS Games
By an Amazon.com customer
ExitExit
Buy new: $19.99 / Used from: $9.94
In order to escape you will have to figure out the precise path using yours and your rescued character's precise abilities. Has clever and well-designed puzzles. One of my favorites. Similar to Toki Tori in the terms of puzzle solving techniques.
PrismPrism
Buy new: $19.99 / Used from: $8.99
It uses simple well-defined parts in increasingly complex arrangements. It's really an excellent logical challenge.
NevesNeves
Buy new: $79.99 / Used from: $18.99
~*~ You are given a silhouette to fill with special shapes. Excellent for improving spatial visualization skills.
GravityGravity
Buy used from: $26.29
~*~ You have to construct objects to get the ball to hit the goal. It's a simple well-done physics puzzler.
Mechanic MasterMechanic Master
Buy new: $26.42 / Used from: $14.73
~*~ Rube Goldberg lives!
Brain VoyageBrain Voyage
Buy new: $20.99 / Used from: $14.54
~*~ Collection of mini-puzzlers, including variations of many classic thinking games.
Honeycomb BeatHoneycomb Beat
Buy new: $7.00 / Used from: $8.99
~*~ Tile turning pattern game. Quite challenging on the later levels.
Rubik's WorldRubik's World
Buy new: $15.24 / Used from: $6.99
~*~ Two of the mini games are really well done thinking puzzles that I greatly enjoyed solving.
PolariumPolarium
Buy new: $7.89 / Used from: $4.74
~*~ 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 used from: $6.78
~*~ Don't be fooled by this game's cute graphics, this is the most challenging spatial logical reasoning puzzle game I have ever played. Do NOT get this game if you are easily discouraged.
Chu Chu RocketChu Chu Rocket
Buy new: $48.98 / Used from: $6.75
Spiritual predecessor to Rubik's Puzzle Galaxy: Rush
Steal PrincessSteal Princess
Buy new: $33.58 / Used from: $17.61
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: $16.50
~*~ 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: $24.50
ScribblenautsScribblenauts
Buy new: $27.96 / Used from: $24.50
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: $15.98
~*~ Has a poorly designed interface but the actual spatial logic block moving game is quite a good challenge.
MatchstickMatchstick
Buy used from: $49.90
~*~ Bare bones presentation, but if you like match puzzles it is still worth getting.
ZendokuZendoku
Buy new: $19.73 / Used from: $8.00
sudoku but with non-numeric symbols
Jumble MadnessJumble Madness
Buy used from: $34.85
~*~ Nearly as good as the paper
Picross DSPicross DS
Buy new: $74.69 / Used from: $16.44
Similar to Sudoko. Good relaxing logical reasoning challenge.
Picross 3DPicross 3D
Buy new: $39.99
Chessmaster: The Art of LearningChessmaster: The Art of Learning
Buy used from: $43.78
good for beginners and intermediates, plus has surprisingly-good mini-games.
Fritz ChessFritz Chess
better for advanced players
Mr PantsMr Pants
Buy new: $16.85 / Used from: $11.70
Brain ChallengeBrain Challenge
Buy new: $134.89 / Used from: $28.89
IMO, the best of the brain training clones. There is also an excellent Wiiware version
Big Brain AcademyBig Brain Academy
Buy new: $59.99 / Used from: $13.99
Brain Age 2: More Training in Minutes a Day!Brain Age 2: More Training in Minutes a Day!
Buy new: $18.24 / Used from: $13.00
Flash Focus:  Vision Training in Minutes a DayFlash Focus: Vision Training in Minutes a Day
Buy new: $21.45 / Used from: $7.75
Brain AssistBrain Assist
Buy new: $12.79 / Used from: $8.49
~*~ Quirky presentation with standard mini-games.
Master Jin Jin's IQ ChallengeMaster Jin Jin's IQ Challenge
Buy new: $39.99 / Used from: $12.99
~*~ 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: $19.20 / Used from: $11.99
Think Logic TrainerThink Logic Trainer
Buy new: $19.99
Not out yet, I'll update this after I try it.