Oh man, that's almost impossible to do without restricting to one per franchise. I will list my top 10, but I will also name a top 10 with one per franchise, because it's going to be a very Mario & Zelda centric list otherwise:
The list I came up with at first without looking at my previous votings:
1. Yoshi's Island
2. Super Mario Galaxy 2
3. Super Mario Galaxy
4. The Legend of Zelda: Skyward Sword
5. Banjo-Kazooie
6. Super Mario 64
7. Super Mario World
8. The Legend of Zelda: Majora's Mask
9. The Legend of Zelda: Twilight Princess
10. Pikmin 3
I decided to follow my format from last time: Two or less per franchise.
1.
Super Mario World 2: Yoshi's Island; The best game ever, simply put. Incredible level design, perfect game design, infinitely charming, great deal of variety. I couldn't even imagine how one could improve upon this sheer time less classic.
2.
Super Mario Galaxy 2; EAD Tokyo at it's best! Once again, perfect game design paired with extremely fresh and playful level design. Also a bit more challenging than Super Mario Galaxy 1. Yoshi also felt great in this game. To me, this game is the pinnacle of 3D gaming and I'm waiting desperately to see, what's next for EAD Tokyo's flawless track record. IMO, it's the most talented studio there is.
3.
Super Mario Galaxy; See Super Mario Galaxy 2. If it were a bit more challenging, maybe I'd even have given it the edge over part 2, but both of them are equally amazing!
4.
The Legend of Zelda: Skyward Sword; The grandmaster of puzzle-gameplay and the most focused of all the Zelda-games. I was really skeptical before release, even thinking that it might be quite low on my Games of this year list (Behind Sonic, Mario, Rayman, Mario Kart) after playing the Gamescom demo. How wrong I was, how great this game turned out. A masterpiece that shamefully didn't get nearly as much credit as it deserves.
5.
Banjo-Kazooie; Wonder why there are still so many people caring for Rare? Well, this right here is the answer, the only platformer not by Nintendo, that can live up to Nintendo's heights in this genre. Awesome level design, cheerful characters, super tight gameplay, classic humor, this game alone is enough for me to play any Rare game in an instant.
6.
The Legend of Zelda: Majora's Mask; The game that defines atmosphere in games. I found this game to be way more frightening than any horror game I've ever played, due to it's wacky design, incredible characters and timeless time-feature. Before Skyward Sword, this was the unrivaled master of Action-Adventure gaming and it was barely edged out by its own successor, Skyward Sword.
7.
Pikmin 3 ; The best game of this generation in my opinion. Fantastic blend of action-adventure and strategy, featuring outstanding world design and fantastic gameplay. A timeless classic
8.
F-Zero GX; The fastest, most difficult, most tight, most intense racing game ever created. Amusement Vision and Nintendo simply was a match made in heaven, the result is a timeless classic that still is my favourite racing game of all time!
9.
Yoshi's Woolly World ; A fantastic return to the console, featuring an amzing level design and one of the cutest looks ever conceived. There are a lot of fantastic 2D platformers on Wii U, but Yoshi's Woolly World is very special among them in my opinion.
10.
Metroid Prime; Metroid Prime is a fantastic expierience with a well thought-out gameplay mechanic and an organic, livid world, that needed to be explored. I absolutely adore this game and I also love parts 2 and 3 of this series.
Only one per franchise:
1. Yoshi's Island
2. Super Mario Galaxy 2
3. The Legend of Zelda: Skyward Sword
4. Banjo-Kazooie
5. Pikmin 3
6. F-Zero GX
7. Metroid Prime
8. Donkey Kong Country Tropical Freeze
9. Fire Emblem Fates Conquest
10. Mario & Luigi: Bowser's Inside Story
Changes from last time: Banjo has risen, Pikmin 2 got replaced by Pikmin 3, Yoshi's Island DS got replaced by Yoshi's Woolly World