These DSiWare games can’t be transferred to the 3DS

From Etrain:
Become an Artist! Easy Sketching
Become an Artist! Everyone’s Painting Series

From Gameloft:
Earthworm Jim
Asphalt 4: Elite Racing
Real Soccer 2009
Real Soccer 2010

From Square-Enix:
Dragon Quest Monster Battle Road V, special color code scanner

From Takara-Tomy:
Nari Kyara Homeroom Teacher Hitman Reborn!
Nari Kyara Naruto: Shippuden

From Tasuke:
At Sports! Pro Baseball 2010

From Nintendo:
Flipnote Studio
Nintendo DS Browser
Pocket Rurubu Series

From Hudson:
Quiz Music Time w/ Karaoke JOYSOUND Wii SUPER DX Song Navi
Sudoku: 50 Beginner Puzzles!
Sudoku: 150 Puzzles!

This list applies to Japan specifically, but you can expect that some of the titles will be nontransferable in North America/Europe as well – Flipnote Studio, the DSi Internet Browser, and Earthworm Jim, for instance.