I enjoyed Majora's Mask better than OoT, I felt OoT was too linear, even with sidequests.
The time system in Majora's Mask was incredible, and gave a sense of real trial and error. The game really made you feel like a pervasive, yet unsung hero; because time reset you would have to reacquaint yourself with a great many characters, but the Nintendo quashed the redundancy by tracking your exploits through the Bomber's notebook.
It was the most free-form Zelda I had ever played, in that the only restriction was that you had to complete things on the game's timetable, which wasn't that bad considering you could warp, bunnyhood, horseride, and/goron to your many objectives. And it managed to be challenging.
I still play 64 games on 1964 and PJ64/k, because my N64 is no longer functional. I use the wired XBOX 360 controller for all my emus.