Don't do it! 
 

I would watch this. 
 

If you have any access to an N64, play it there.
 
If you have access to a GCN and the Collector's Edition disc, play it there instead.
 
Only then should you go to the 3DS.

I think you should wait until it's actually out on 3DS to ask this question, more people will know the actual differences then. 
 
If you were able wait until now to play it, you could probably wait a little longer.

....how did this happen? How have you not played it? 
 
You could wait or you can find a copy of the gamecube refurnished rerelease and play it on a GC/Wii. Or play it with worse resolution on the N64. Just play it!

Mainly because of the graphical improvements, the 3DS version will probably be the best version to play when it comes out.

I guess. I kinda hope they change some stuff though, because a lot of people have played that game once or twice.  
I don't even like the 3D Zelda games as much as most people seem to and I've both played through and watched a friend do a playthrough of the game. 

Well it will definitely be more expensive.

I would wait until some more information surfaces on the 3DS version. At this point in time, it looks like it will be the best looking version, but there could be some serious control issues to deal with.

That said, if you have access to a GameCube and can find one of the two discs released with Ocarina, that's the best version out there right now.

I wouldn't try and go back to the N64 version. Without nostalgia to blanket your senses, it's an ugly game by today's standards.

I'm also in that tiny camp of people that have not played it. I'll probably try an emulator sometime soon.

I'd get the 3ds version for the simple fact of the Water Temple being less of a pain in the dick.

Go ahead and play the version that looks the best. Even if they redo some of the game's segments, you'll get the basic idea. I can't imagine anything being changed too dramatically. Plus you can better justify your playing time on a relevant system and release. Considering the game is widely accepted as the greatest game of all time, it's your duty to play it. 

A smooth framerate and better animations make the 3DS version the optimal choice. Seriously that framerate blew my mind when I first saw it.

Ocarina of Time is my favorite game of all time, and I love it in its original format... But if you've never played it before, I would imagine that the 3DS version will be just fine, if not the best way to go. Improved visuals, portability, easier inventory management...
 
But like others have said, you may want to ask again when it's actually out just to make sure.

The gold cartridge N64 version is the best one.  It had the best music for the Fire Temple.  They changed it later on because it apparently had an Islamic chant in it or something like that.
 
That said, any version will do because that game is awesome and has aged fantastically.  I played through it for about the 7th time about 6 months back and it was still awesome.

" @Aus_azn: Why is the 3DS going to be the worse one? I actualy do own a N64, but I thought it would be better to just play it where its gonna look better. "