i have yet to play the 3DS version but i have to say that the original OOT that came out for N64 is my favorite. no matter how many times i beat that game, i still love it.
I would have to go with the Original Gold cartridge version 1.0. It was so much fun playing with friends and do the Swordless Link glitch. We would have hours and hours of fun seeing what all we could do with it.
The 3DS version is amazing, but I'll always love the 1.0 version. I never realized it was special until recently, but I do love my gold cartridge, uncensored version. <3
All the stuff on that original Gold v.1.0 cartridge is a story of its own. The N64 logo on the title screen is oddly bright, there is some kind of muslim chanting in the Fire Temple, there's a Muslim-like symbol on the Mirror shield, Red blood, etc. I love this cartridge and I still play it all the time
The very first one, (the gold one) I love the Chant in the fire temple, and even if they did have to remove it, I remember it making the whole temple just that much eerier~