I've heard that the NES VC games have a multiplayer option. But I can't seem to get it to work with my sister (who also have the 3DS and the games). What am I missing?

You can only play multi-player games with alternating play modes.
That is, you push L+R+Y (I think, check the built-in Manual to be sure) to swap the 3DS between player 1 and player 2.

I think multiplayer isn't in the games yet. If I'm not mistaken the games will receive an update later on when they are released to the public that will allow multiplayer features in all the games that has the option for it. As of now it's not available.

I think they were going to add wireless multiplayer in the update at the time when NES games come available to everyone.

And there's also that Contoller changing thing that was already said. Good for turn-based NES games. (Tried playing Ice Climbers and had some problems to control both players at the same time xD)

Ok. So I've got to wait for the update. Turnbased doesn't sound that exciting for some games.

It'd work with golf and super mario bros.

But I can't wait to get a LAN update so I can do some serious ballon fighting.