I voted for Majora's Mask and Super Mario 64.
Majora's Mask is my favorite game of all time, so I get a little frazzled when I see that OoT gets all the special treatment, but MM doesn't. I mean, come on! You can't just remake Ocarina of Time and leave the Majora's Mask fans hanging! Those two games pretty much go hand in hand, in my eyes. Of course, I am more than happy that Nintendo is remaking OoT, but I'd be even happier to see a Majora's Mask remake as well. I think Majora's Mask also has visuals that fit 3D better than Ocarina of Time anyways - the surreal imagery, the moon, the masks! Imagine slapping on the Zora Mask in 3D. Wouldn't that be great? I also voted for Super Mario 64 because, well, that game's a classic. However, I think the blocky visuals are showing the game's age. If it were remade with Super Mario Galaxy's visuals, I would be in heaven. Plus, you can't remake the most popular Zelda game without remaking the most popular Mario game, now can you?
However, I really don't think The Wind Waker needs to be remade, nor does it ever need to be remade. Nearly 10 years later, that game holds up incredibly well. The visuals are still as crisp and clean as it was on the day it was first released. I think the graphics of TWW are meant to look cartoonish and undetailed, so there's not really a lot that Nintendo could do to improve it, visually, without compromising its unique visual style. Unless you mean an actual remake of the gameplay mechanics themselves, The Wind Waker possesses no need for a remake.
I've never actually played Golden Eye, though I am well aware of its enduring popularity. Since I have not played it, nor do I have any interest in playing it, I'm relatively indifferent on a Golden Eye remake. As for the Oracle series, I don't think they need a remake. Remaking 2D games seems pointless to me, especially if the graphics are already sufficient. Remaking them as 3D games would also be silly. Games that are meant to be in 2D should stay in 2D. I just can't see a 2D game working as a 3D game, since the gameplay mechanics are very different between the two.