The ? one is for games(The shooting one, unless there will be more). The character ones are for taking pictures of the specific characters on the card(including Miis). The only other card known right now is the one that comes with Nintendogs + Cats which allows you to bring your pet into the real world.
I would hope they would at some point make some that allow you to use multiple cards to mark as way points so then you could say, control Mario and have him jump around your house as the 3DS generates blocks and enemies. I honestly don't see that being too hard with their technology.
You can use them to take pictures of the characters on the cards and make it look like they are in real life. For Nintendogs+cats you can use the "?" to make your pet "Come alive", and if you switch that out with any of the character cards it will show your pet wearing some type of hat/accessory relating to that character. The only other AR things I know about are Target Shooting and Fishing.
If video recording does come to 3DS, then I guess it would be a possibility to make videos of Nintendo character hanging out on your table. Who knows? There's so much to look forward to about the 3DS, and still so much to learn about it.
1 idea is maybe a battle field where you put two of your cards down and they will fight it would be so cool like link vs mario,mario vs kirby and things like that.