I forgot to give my own opinion as well!
For me, it's a tie between the original/1.1 for N64 and the 3DS version. But I'm kinda leaning towards the N64 because of several factors, including nostalgia, authenticity, and controls. OoT feels like it was designed for the N64 controller, not the 3DS. But the graphical enhancements of the remake make it much more pleasing to the eye than the original. Hyrule Castle Town no longer felt like a creepy, desolate place with it's dark color scheme; it was transformed into a bustling, joyful place filled with vivid colors. It's a shame they didn't even touch the music, though. It could have been amazing had it been remastered.