The app is free, so check it out: QR MyDesign Assistant for Animal Crossing 3DS by Bochen Technology co. Ltd.
If you know of any other programs for PC or online that do the same thing, let me know! And feel free to leave any QR codes you've generated using this app in the comments. Here are the ones that I've made.
Update: An online app for making designs that's in Japanese. (Doesn't do QR codes.) (Link)
Update: An Android version. (Link)
Update: An English downloadable version for PC is now available and in development. (Download (v.0.4 7/9/13), On Reddit)
Update: Another web-based app, but this one can generate QR codes. (Link)
Update: A web-based app that was submitted in the comments. Thanks, Jason W.! (Link)