I have version 1.0 with the chanting. I just got this copy because someone accidentally sold the one I had. Getting to the Fire Temple and finding out my new one was the original was a lot of fun!
3DS version. It's the same great game with 3D, portability, and better graphics. The only problem I had was the fact that the whole "press ^ when falling to do a roll when you land to take no damage" didn't work very well.
I was torn between the original NTSC V1.0 version on the N64 and the 3DS remake. The original was such a fantastic game and such a fresh perspective on the Zelda Universe. I was very impressed with how much the updated textures added to the 3DS version. The 3D mode also added to my enjoyment of the 3DS version and I really like the addition of Boss Battle mode. The controls where well done on the 3DS (although I was a little frustrated with gyroscope aiming). The thing that made the biggest difference to me was the ability to take one of the best games of all time and play it anywhere.
the 3ds added a better look on a truely amazing game! the graphics being what they are make it feel like a new adventure without even starting up the game!
The 3DS version. It is almost exactly the same as the N64 version, with updated graphics, and the controls are a bit better. The only difference that I can find besides these would be the Sheika stones, but this is a good thing for the younger generation.