Majora's Mask and SotE are my best choices.

I´ll go with Paper Mario. Sticker Star seems to be okay - good, but nothing can beat the original and The thousand-year door

Majoras mask I guess, Mario 64 and OoT have been done.

I wouldnt say no to FZero X or WaveRace 64 but then again I'd rather sequels

Majora's Mask and Banjo Kazooie would be the two obvious titles.

Banjo Kazooie would require licensing from Microsoft, but that has happened before on the DS, so it's not out of the question for 3DS.

Majora's Mask!! Omg I would cum in my pants so bad if that happened.

Banjo and a DK game (2D or 3D)

Yeah, I will also say Majora's Mask. Mainly because most games I want to see remade were created by Rare, but also since it doesn't make sense to remake games like Mario Party, Super Mario 64 (already remade), F-Zero (I'd rather see a new entry), Mario Kart, Pokémon Stadium/Snap, Super Smash Bros., etc. Majora's Mask is the perfect fit.

I spent hundreds of hours playing Ocarina of Time 3D, and I wouldn't expect to spend less time on this game.

F-Zero X...

Mystical Ninja Starring Goemon and Mystical Ninja Starring Goemon 2.
In a collection.
Please.
Seriously.
P-l-e-a-s-e.

It's because of the Star Wars Christmas Special .

OT: No more remakes should be made. The two that are there now were the ones that would've benefitted the most from the improved hardware anyway. That said, the inw that's most likely to ever happen would of course be Majora's Mask. The framework for it is already there. Mario 64 would be a good one to remake in it hadn't been already on DS. All the others would be pointless as it would add nothing to the game and you could just as well just make a new entry, or are impossible to happen.