I have the NDS Adapter Plus and so far I have been able to backup and restore the following:
Pilot Wings Resort, Ridge Racer, Steel Diver, Lego Star Wars Clone Wars. It does not recognize Madden 3DS so far. Yes, I am of course using the latest firmware 3.x for it.
Since we are talking saves here: I also am still researching the 3DSavetool with tweaking game saves but there is more to it than just the save check sum that is a problem so far. I am not so sure the decryption tool in that program does a good enough job. Also, so far there is some evidence the AR code types basis is still being used. The work is ongoing to determine what new code types are going to be needed, if any for the 3D.
There is much work ongoing for dumping the 3DS rom, code types, and full implementation in DSi and 3DS modes respectively for many flash cards. I am concentrating on the iEVO for the time being.
ciao