FF6, FF7, FF8, FF10, Xenogears, Chrono Trigger, Dragon Quest 8, Xenosaga Trilogy, Earthbound, Soul Blade, Illusion of Time, Terranigma.

Majora's Mask, especially. It wouldn't be hard, taking already made models from OoT 3D and some textures and such. Would they be able to do it in a year you think? :P

FFVI, one of my favourites. It would be awesome!

These are perhaps (maybe I would rather have completely new games): Terranigma, Super Mario World, Super Mario RPG (or maybe a new one)... Anyway, the two aboves are the ones I'd want.

Sega

Shining Force 3 (I'm still pissed that Bernie Stolar only had one of the three chapters localized.)

Phantasy Star IV (One of my favorite JRPGs, it would be nice for it to get an update and proper translation)

Panzer Dragoo Saga (Great game that too few people had the chance to play)

Daytona USA (Only if they included the J-Pop Sound track)

Nintendo

Wave Race 64

Eternal Darkness

Capcom

Bionic Commando

Square/Enix

Actraiser

Final Fantasy VI

Konami

Metal Gear (I only got to play the NES version when I was a kid)

Metal Gear 2 (Never got to play the real Metal Gear 2. The NES sequel doesn't count)

That's all I can think of off the top of my head.

Metroid II.

River City Ransom.

I'd also go ga-ga over a modernized remake of Axelay:

Epitome of shoot-'em-up action, I tell ya. Plus it could actually make pretty good use of the 3D effect. (For those who care about that stuff.)

There are actually quite a few games from the 6th and 5th gens that I wouldn't mind having available on the go with some tweaks and improvements.

Visual improvements over the originals (like OoT which has aged pretty horrendously like most 5th gen polygon games) would be totally welcome.

I don't know if I'd pay $40 for them, but I'd probably pick them up for the second time down the road once discounted.

I was actually pretty glad when Chrono Trigger was re-released for the DS as it was one of my favorite SNES titles.

I was also glad to have Zelda Link to the Past on the GBA.

It has been nice having SSFIV on the 3DS even though it has minor downgrades (mainly the still backgrounds) and the tiny D-pad on the device is pretty far from ideal. The pick up and play nature of a handheld makes it perfect for 20 minute sessions.

I'm hyped about playing MGS3 on the 3DS, even if Konami adds next to nothing (unlikely) and it's just a portable version of the PS2 game with 3D depth.

Wouldn't mind a redone FFVII at all.

So I don't have a problem with the 3DS being a 6th Gen portable console assuming it still gets "all new" exclusive games that make the most of the hardware as well.

OMG yes to SF3 and PS4 and FF6 and Actraiser! And Panzer Dragoon Saga! But mostly SF3 and PS4, 2 of my favorite games ever. I want the other scenarios too. 

Dragonforce 1 2, Guardian Heroes, and the good version of Castlevania: Sotn too please.

Final Fantasy 4, 5 and 6 in 3D would be pretty sweet, and seeing as they can do Metal gear solid from ps1 on 3ds, Getting Soul Reaver 1 on there would be great. If they could get those then I would actually buy a 3ds. At the moment my nintendo products seem to have a habit of gathering dust (I suspect my Wii would catch on fire if I turned it on, its been so long) so I can't justify another nintendo purchase just yet.

I'd love to play a remake of Majora's Mask. Add a few more temples, more items and side-quests, and I'll buy it and a 3DS!

I can't believe I forgot Dragonforce and Guardian Heroes. I'm ashamed. Add them to the list too.

All three Mother games would  be nice, and I want them actually released in Europe considering none have so far...