Darkflame said:
Actually, I think its all the NES games - I had a update option for all of them when I looked.
Not seeing the scanned manuals though, just the
save states added :-/*edit* seems a mistake in my region/timing. The others didnt update despite the fact a update was listed and they greyed out for awhile.(I had all 10 set to update when closed)
For some reason the ambassador certificate itself had a update too. (what does that do?)
Also; random 3ds thing
"Nikki" the character that guides you in the letters page sneaks into you Mii Plaza list!
The other games were indeed updated, this was just to add compatibility with certain SD cards that were having problems with those games, it was talked about on GBATemp, I believe. I saw it on NintendoLife though.
I think the update for the ambassador certificate was just to enable you to recieve notifications when the other games have been/are going to be updated. Or it could just be a compatibility update as well.
Update all your games and apps, just to be sure though. I've done it all, and I'll regularly check my downloads for any more updates. Hopefully Nintendo will fix the "Available Updates" section soon, it's not worth it being there if they don't.
Also, I noticed that Nikki appeared in my Mii plaza today, haha. 
EDIT: @Stulaw and Marzy, the updates for Pokédex 3D and Balloon Fight were just compatibility updates as well. Well, I know Balloon Fight was for sure. I'm pretty certain that the 'dex 3D update was just for compatibility issues too. 
( Edited 17.02.2012 15:01 by Mush123 )