When the 3DS eShop channel launches on June 6th (NA) you will be able to transfer some of you already purchased DSiware games. (Well over time) Nintendo did mention that a few games will not be transferable and this list, from Nintendo Japan, has been released. I am not sure if this list is the same everywhere but I assume it will be close.

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!

Link