Yesterday I got SMB 3Mix in my Nintendo 3DS, injected in a .cia by a program called Ultimate NES VC Injector for 3DS. What this program basically does is, in order, taking a .nes rom, taking its data from a database or custom data (title, short title, publisher and icon), selecting a banner, a Title ID and a screen mode and, finally, injecting it all in a CFW-installable .cia.