Update: Nintendo has released an official list of the 11 DSiWare games that cannot be moved to 3DS, superseding this list.

Original post: Nintendo always maintained that "most" DSiWare games would be transferable to the 3DS, but naturally not all have made the grade. According to IGN, these are the 19 games staying put on the DSi:

Whether or not these games will be available to download from the 3DS DSiWare portal remains to be seen, but for now, we welcome theories for why these games are unable to be transferred.

[source uk.ds.ign.com]