@KingMike most 3ds ROMs, which for the others in the crowd use a unique key for every ROM, from the better sites are left in encrypted form as that was how the earlier flash carts (and some current ones) work, to say nothing of general scene type rules saying it should be as close to the original as possible.
The decryption files themselves are (were? rxtools changes a few things) known as XORpads as they are basically a match to the ROM but if you XOR it against it then you get the decrypted version, and being XOR you can encrypt it again though more on that later. Both file size and it being basically a ROM/ROM specific decryption key mean few will distribute the XORpad either.
There are some sites out there which distribute the decrypted version, various reasons for this though about the only "good" one is the citra emulator needs such things if you are going to fling commercial games at it. If the game has otherwise been hacked then it might be found in a so called 0 key encrypted form (the encryption is done again against an all 00 key), the editing might also have been done in place and encrypted again with the original XORpad.
That would probably then leave the CIA stuff. http://www.3dbrew.org/wiki/CIA
if you want to get technical, though 3dbrew is anti piracy so they nerf things a tiny bit. Short version there is the 3ds is a system with at least aspirations towards being a modern computing device and can install games on its NAND/SD card and the CIA format is used for that. Functionally there is little difference between a ROM and a CIA file so you can convert. I am not particularly up on the current stuff here (the custom firmwares on the 3ds are getting better and may have left "only for penniless masochists" territory but they are by no means production grade) but it is likely not going to do much good for the OP.