According to GBAtemp.net, the affected carts include (but aren't necessarily limited to) the Acekard 2i, Supercard DSTwo, M3i Zero, iPlayer and DSTTi. A handful of carts are reportedly unaffected by the update, including the EZ-Flash Vi, iSmart DS and Hyper R4i.
And thus the cycle begins anew, with hackers diligently hacking away at Nintendo's new anti-piracy efforts (which didn't take too long last time). Joystiq does not condone piracy, but flash cartridges also have plenty of legal, entertaining uses. For example, did you know the DS makes a handy SCUMM emulator?