edit: lol i just noticed voting is closed. well at least i wrote some words for posterity
1) Super Metroid; The first time you play Super Metroid, it's an experience. The tasteful, understated storytelling at a time when games were still trying to find their legs for that sort of thing. The creepy sci-fi ambiance, and the incredible music. The sense of isolation, and hostility on a planetary scale. Samus' huge, bounding leaps and graceful zero-gravity falls. Even when you aim up or down with the shoulder buttons, she's looking where she aims--she's exploring the world in the same way that you are, taking it all in. It's a sense of immersion that might seem primitive today, but at the time was completely unmatched.
The next times you play Super Metroid, it's a fucking video game. And what a video game. Some might say it's the greatest video game ever made. Some of these people might even name their NeoGAF accounts after obscure enemies from it. A veritable trove of secret abilities and weird physics quirks give players the ability to bend the game to their will. High-level play is rewarded with sequence-breaks-- fighting bosses in arbitrary orders, collecting powerups far earlier than one should-- and the game is always ready to handle the load (unless you try to shinespark Kraid, but that's a story for another day.) As speedrunning becomes an increasingly-accepted way of interacting with old video games, it feels important to highlight just how flexible Super Metroid is-- there are few games with as many potential routes or rulesets one can take in general, to say nothing of other platformers in the year 1994.
2) The Legend of Zelda: A Link to the Past; Super-era Nintendo had a thing for taking their flagship titles on the NES and using their shiny new hardware to basically make "that game, but ten times better." While one can sing the praises of Zelda 1's completely open structure, or Zelda 2's crazy gaiden-level reimagining of the series, neither game can hold a candle to the third Zelda title in the realm of design. This is the epitome of master craftsmanship. Super Metroid feels like it turned out as good as it did almost by accident. Nothing about A Link to the Past feels like an accident. It's almost good to the point of being boring, but excessive quality beats boring every time.
3) Metroid Prime; Speaking of games that turned out good by accident... People didn't even expect this game to be good! Generally, when franchises made the difficult transition from 2D to 3D, bets were hedged. The Legend of Zelda: Ocarina of Time is almost exactly what you'd expect the first 3D Zelda title to be. Metal Gear Solid is almost literally just a 3D remake of Metal Gear 2. Metroid Prime had the benefit of a fresh-faced studio with a thing or three to prove, and five-ish years of dimensional-transition work before them to draw on, and the result is a game that doesn't look like or play like what anyone would have expected a 3D Metroid to. Miraculously, it hits all the right notes-- it's not Metroid, but it's Metroid. And it's also really good.
4) F-Zero GX; The purest expression of speed from a series built almost entirely on purity of expression of speed. A ball-bustingly hard arcade racer with extremely technical mechanics that doesn't just reward mastery but practically expects it. A super-cool machine-building mode. The beautiful absurdity of an F-Zero story mode with CG cutscenes. This game has it all.
5) Super Mario World; "Super-era Nintendo had a thing for taking their flagship titles on the NES and using their shiny new hardware to basically make 'that game, but ten times better.'" This comment is slightly disingenuous, because Super Mario World isn't exactly ten times better than Super Mario Bros. 3, a game to almost make my list and which will surely make others. But the point remains: there are a lot of great Mario games and this is the best one. Its placement is self-explanatory.
6) Fire Emblem Fates: Conquest; Fire Emblem is one of Nintendo's longest-running franchises, even if we in the West haven't always known that. It's been such a highly-iterative franchise for such a long time that you'd almost have to assume they'd have cracked the code and made the best one of these a long time ago, on the Super Famicom or something. This seems like a series that should be spinning its wheels at this point, but oops-- Fire Emblem Fates: Conquest is, from a design standpoint, the best Fire Emblem game yet. Who'da thunk? It manages to take all the neat features of recent FE titles and graft them onto maps that ought to be making even the most ardent Thracia fans weep in joy.
7) Bayonetta 2; A rock-solid followup to Bayonetta, one of the greatest games of all time. It even has that game included! Character action games have ended up a pretty niche genre, but for the people out there who like them, the Bayonetta titles are some very lovingly-crafted, smartly-designed, well-tuned ones of those. You might have your pet games in the genre that you like more, but as far as Nintendo-published games go, it's the tops.
8) Pokemon Gold; I haven't kept up with Pokemon for a while now so I'll admit this one could just be straight-up nostalgia, but as far as I'm concerned no Pokemon title has been as huge a leap forward as this one and its sister games were over the originals. And it's fucking enormous too. Sixteen badges? Too good for this world.
9) Star Fox 64; The Nintendo 64 is a dark spot for Nintendo in my eyes. Their first party output was inconsistent and the third-party support was non-existent. I have a hard time keeping reverence for all the commonly-revered N64 games. This one is pretty hard to take issue with. Super fun arcade-style shooting action wrapped in an adorably campy presentation. At the time it might've seemed like poor value for the price of an N64 cart, but removed from price concerns all we've got left to judge a game by how fun it is. No N64 game is as fun, in my mind, as Star Fox 64. Its shortness is irrelevant when I always have fun playing it.
10) The Legend of Zelda; Majora's Mask; The Zelda II to Ocarina of Time's Zelda I. A few games have tried to do the Clock Town thing since, but somehow nobody's ever seemed to top it (that I've played, at least.) When I'd beaten Ocarina of Time a couple of times as a child, I often found myself just running around Castle Town, or Kakariko Village, and trying to imagine what a day in the life was for these NPCs. Virtual people-watching with a healthy dosage of imagination. Majora's Mask was pretty much made for me, in that regard, by actually doing the imagination part for me, and then dumping a veritable trove of goofy, quirky, fun, exciting side-quests to flesh out an otherwise-thin Zelda adventure. And Stone Tower Temple is one of the best dungeons in the entire franchise. It's no Link to the Past, but what is?