HA - It's funny you talk about Majora's Mask, because that is one that I'm playing through right now. About half-way through the game, and this is traditionally how far I make it before getting distracted and moving to something else... but I like the game a lot and think they didn't a nice job updating it. (Changes that I've noticed make some things feel a bit more convenient - but nothing seems all that significant.)
The game I'd like to see, even though some aren't really sequels, include:
* Crimson Shroud really deserves a fully fleshed out sequel. Despite one specific rough spot, the game is a fantastic adventure. I'd love to see if this design could be expanded into a full, deep campaign.
* A Professor Layton Trilogy compilation, packing the first three games into a single 3DS cart. Recently saw a few of these at a second-hand shop, and thought long and hard about buying them due to strong nostalgia for Unwound Future.
* Something in the same style or universe as the wonderful Ghost Trick - what a wonderful game! A true sequel might not make sense, but maybe Missile could lead a game?