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Link's Awakening/Oracle of Ages/Oracle of Seasons

These games are great, we all know this. I personally do not think Nintendo is ever going to give us a better platform to own them. And heck, the 3DS form factor is pretty great, what more could you want?

Lufia: The Legend Returns

This is an incredibly underrated GBC title that I literally forgot they put on the eShop until just now. I just shelled out some serious cash to buy a physical copy, don't be like me, just download it here.

Lufia: TRL is a turn-based RPG with some really intriguing party mechanics; basically you have up to 9 members out all at once, in a 3x3 grid, but only one member per column can attack. Their row determines how much damage they take, and how much they deal with melee attacks. The frontmost 3 need to be tanky, because if they die you lose. There's some interesting situations where enemies can catch you by surprise, causing your formation to be rotated when you start, its fun. The writing is goofy, the artwork is gorgeous; if there's any downside its that the dungeons themselves are fairly lackluster proc-gen layouts. Still, I think this is an unmissable game.

Shantae

This is available on Switch, yes, but I think pixel games just look nicer on the 3DS screen tbh.

Shantae and the Pirate's Curse

I don't remember if this one is on Switch? I might do some research, probably not though. This is a really cool metroidvania Shantae title, not too hard to 100%, not insanely long. Pretty ideal metroidvania in a lot of ways.

Dillon's Rolling Western

If you slept on this one, wake up. This is an extremely enjoyable and interesting genre mash-up that uses the touch screen interface to pretty good effect. It came in the middle of a huge drought of new Nintendo ips and I really wanted it to take or more than it did. Its fun, it gets pretty difficult near the end, the characters and enemies all look really cool. There's a sequel, its probably good but I haven't played it because there's a character with a Mii head and it looks really bad, lol.

Severed

Severed is a beautiful and spooky dungeon crawler from Drinkbox Studios that benefits majorly from the 3DS touch screen. It's on some other platforms, but I really do think this game works best with a stylus.

Fairune 1 & 2

These are also on the Switch, however as I said before, little pixel games look better on the 3DS screen to me. Surprisingly deep and yet trimmed-back top-down RPG adventures with beautiful art and great music. Fairune 2, in particular, is an absolute treat. They really reduce the genre down to the bare essentials in a way that I actually find extremely satisfying. Oh and it has a shiny-hunting equivalent where certain areas have a chance to spawn a super-rare monster purely for the sake of filling out your beastiary, which I adore.

Crimson Shroud

Crimson Shroud is an interesting one for me because I have been stuck at the same, fairly early spot, for years and literally can't even find the answer online. If you've beaten this game, please help me! Anyway despite that, this game is extremely cool. I truly believe it's not broken and that I'm just stupid.

1001 Spikes

It's on other platforms, it looks better on 3DS, its really really fun.

ikachan

A short and sweet metroidvania from Studio Pixel. This game oozes charm, I cannot recommend it enough.

Xeodrifter

Another miniature metroidvania, although this one is a bit meatier than ikachan. Really fun, really cool, it's nothing crazy but its just really well made.

Shovel Knight

Okay this one is more than the usual "it looks better on 3DS", the 3D effect is delightful and I really do think it makes all the difference.

Minecraft

It is not fun to play on 3DS but they supported it for a surprisingly long time and I think low-spec ports are neat.

Harold's Walk/Harold Reborn

Charming and kinda creepy indie 3D platformers that I really really hope are gonna get ported to other platforms because they really should not die with the 3DS.

Legend of the River King 1 & 2

Super cool series of fishing RPGs on the GBC, I loved the first game as a kid (once I got the hang of fishing). The visuals are excellent, really pushing the GBC. The rivers all have complicated currents (that you have to navigate by raft later) and I just think all the animated tiles look really cool.