I just wanted to ask about the other way round, ie. DSIWare to NDS . Anyways, of course they don't work on a 'regular' DS flashcard, because these run in DS mode. DSi has additional features (camera, f.e.) that are only accessible in DSi mode. There are some retail cartridges that access these additional features, and there should also be some flashcards that can. You will need such a flashcard that is also capable of running DSi enhanced roms (only a selected few are). I'm not sure, but the Acekard 2i might work.DS flashcards can not run decrypted DSiware (trust me I tried). And we can already decrypt DSiWare (it has been done, I have 113 fully decrypted DSiWare titles on my PC right now).
Emulation can also be done with No$Gba.
So really Cia is the most important thing (as far as DSiWare is concerned anyways.)
Anyways, could you tell use how to do the .CIA to .NDS conversion?