You forgot all the Pokemon remakes and i don't think Mario Kart 8 DX is a remake, it's an upgraded port.

Anyways i think Samus Returns is definitely one of the best Nintendo remakes i've played, Zero Mission as well these games added more to their original games than any other Nintendo remake i can think of.

I like how the pokemon series has a constant line of remakes of past titles along side their mainline titles. It introduces old regions/pokemon to new generations something I experienced first hand with my favourite game being Pokemon Leaf Green.

Ocarina of Time 3D for me, because it looks nice (Especially when emulated) and it's mostly faithful to the original, unlike Majora's Mask 3D, which had a lot of changes that I didn't like much.

Edit:

Please port this to Switch, Nintendo =P

Zero Mission, all the way for me. It’s a huge improvement over the original, one of the best games ever made, and the rare “remake” that could be classified an an entirely new game.

Zero Mission and Samus Returns. Both remakes fundamentally improve the originals

Yeah, it's a remake of Fire Emblem Gaiden. 

OT: Ocarina of Time 3D for me.

I like Samus Returns too, but in the end I think it’s an overrated remake of an underrated game.

Based on what I like to play, Super Mario All Stars wins with ease. But I really like Zero Mission as a remake.

Fire Emblem Echoes - Shadow of Valentia

I'd have to say Super Mario (ᴾˡᵃʸˢᵗᵃᵗᶦᵒⁿ) Allstars (ᴮᵃᵗᵗˡᵉ ᴿᵒʸᵃˡᵉ)

Specifically the Super Mario All-Stars + Super Mario World version, with the updated version of Luigi since I liked that he wasn't just a palette swap mario in that one. One of my favorite games ever. And in my opinion the best way to experience those games in general.