Go to GodMode 9 by holding Start and press the power button, SYSNAND CTRNAND, title, the entire stuff that is needed for Home Menu.
Anyways, you have to dump them one by one. I tried dumping the entire folder and it won't run well. Sooo, dump them all as CIA approx 1.5 hour. After that, you install it with the Install CIA on the emulator.
If you want to know the listing of those titles, go to 3dbrew and go to Title List for 3DS.
Now about stuffs like Homebrew Launcher or Mario Kart 7 digital copy showing in Home Menu, go to the previous page as I mentioned about Home Menu and showing those installed apps on the Home Menu. Ignore the presents though. It requires NNID and internet connection to access those.
Edit: my mistake. I thought this is the Unofficial Build thread. So uh. Go to the Unofficial Build thread as my post was there.
http://gbatemp.net/threads/citra-unofficial-chinese-builds-discussion.431974/page-350#post-7734160