My favourite dungeon mask used to be the Zora Mask. I spent a lot of time just swimming in the Great Bay, leaping like a dolphin above the surface. Since I can no longer do that in Majora's Mask 3D without using all of my magic, I've found myself enjoying the Goron Mask a lot more than I used to. Goron rolling was always a treat and now I use that to get around more than anything.
My favourite side-quest mask is the Bunny Hood, and not just for the convenience of moving twice as fast.
No, I love the Bunny Hood because it turns Link into a green blur that rushes around Termina, no doubt scaring the ever-loving poop out of the people. I, like most people, play the game with the Song of Inverted Time in effect. The song slows time down to roughly half its usual speed. The NPCs move slower when the song is in effect, so they can keep on schedule. Link, however, moves at his normal speed. So, to the NPCs, Link appears to move twice as fast as normal. Throw on the Bunny Hood, which roughly doubles Link's speed, and he'll be moving four times faster than normal, relative to the people of Termina. This must look exceptionally weird to the humble folk of Temrina, and it makes me smile to think of this every time I play the game.