Some games are incompatible with 3DS DSiWare

Not all titles may be used on DSiWare 3DS, tells Nintendo. The company has not provided guidance to Japan this regard, but has compiled a list of games that will not be compatible with 3DS: eShop service will be available next week on 3DS.

• These DSiWare games can't be transferred to 3DS (02/06/2011)
• List of Non-Tranferable DSiWare Apps on eShop (02/06/2011)
• 19 DSiWare Titles Won't Transfer to 3DS (02/06/2011)
• Intrinsic Games Announces 'Amoebattle' for DSiWare (01/06/2011)
• Antipole coming to DSiWare, PC version in the works (30/04/2011)

List of DSiWare games and applications (wikipedia)