Update: Several titles have been removed from the list.
http://www.nintendoworldreport.com/news/26505
Along with the reveal of the 3DS's eShop lineup in North America and Europe, the titles that will not be transferable have been revealed. Players will not be able to transfer the following games and apps to their 3DSs once the firmware update hits in June:
Update: Since the original posting of this article, the referenced list on Nintendo's web site has been cut from 19 titles to 11.
Most of the games are from studios that have folded (I know that's the case for Pinball Pulse)
That's too bad about Pinball Pulse (one of the best games on the service).