I just finished Majora's Mask on the 3DS this weekend. It was fantastic again although my memory of half of the game from the N64 version was nearly completely gone.
I clearly remember the first half of the game; the first two dungeons. The second half I have nearly no memory of. I remember a lot of the side quests, and definitely getting the very last mask before.
I find it strange not remembering half of a game but I suspect I only played it through once rather than, for example, the many times I played though Ocarina of Time on the N64.