Decided to mess with this myself for something to do...Just thought I'd share this bit of info with the community. I was able to convert SMSAdvance gba packed with complete romsets of Sega SG-1000/GameGear and Master System into CIA using tools from here. I can now run every game for those sega systems on my 3DS. Also had some good results with PocketNes and Cologne(ColecoVision Emulator) and NGPAdvance(NeoGeo Pocket Emulator) and PCEAdvance(PC Engine Emulator). So more complete Retro CIA's could be around the corner. I will not be posting links to my files on GBATemp for obvious reasons but anyone interested can search through 3DS boards elsewhere and find them.
I hope this encourages continued homebrew development for the 3DS scene (Especially the emulation brew!).
How do you go about making the footer for it (any homebrew i guess, smsadvance atm) to build the cia?