Updating my post with info people have shared about games played pre-banning. Thanks to Lordjontan, FreddyBeckett, Dayfid and Nirmonculus for the additional reports. From those, it seems like the following games are commonly used with public headers before banning:
ANY Pokemon Game
Super Smash Bros
Mario Kart 7
It also definitely seems like the bans are not being dolled out for anyone/everyone using the same public headers for these games, and there is no rhyme or reason yet as to why specific users have been banned. Any and all retail/eShop games after banning do not work.
We are still waiting for updates on the following scenarios:
1) Using a NNID from a banned 3DS console on a new or unaffected 3DS console.
2) Swapping out the WiFi module from a banned console for a fresh one with a different MAC address.
If any of the following show up, it also expands the range affected:
* Anyone using a private header getting banned (yet to have a confirmed report)
* Anyone getting banned during a particular game with a public header (had a few reports, none narrowed down to a single game or instance for an elongated period of time)
* Anyone getting banned using a cia (yet to have a confirmed report)
Thanks to everyone who keeps bringing in new information. As for those asking questions about "what if I" or "I've done suchandsuch" asking about likelihood of banning, it is highly recommended to use private headers or play offline only until more is discovered about the causes, extent, and ways to subvert the current type of bans.