Kid Icarus Uprising, Warioware Gold, Smash Bros. and even though it's a remake/remaster Ocarina of Time 3D.

The 3DS remakes of N64 games like Ocarina of Time, Majoras Mask, StarFox etc' are probably the "definitive" versions of those titles.

It's a shame they never got ported over to Switch.

Probably Dragon Quest VII. I didn't play a lot of 3DS. One of the worst Nintendo handhelds I have owned. Played my Vita far more and still do. I have my 3DS still but not turned it on in a few years. Should prob check the battery if it's bulging?

My Top 10:
Xenoblade Chronicles 3D
Mario Kart 7
Animal Crossing: New Leaf
Monster Hunter 3U
Monster Hunter 4U
Radiant Historia PC
Fire Emblem Awakening
Zelda: Link to the Past remaquel
Fire Emblem Fates
Rune Factory 4

Overall, the winner is Xenoblade Chronicles 3D. It wasn't the first time I'd played the game, but I definitely appreciated having that one on the go, as during that time period I was commuting for over an hour each way... 3DS and my E-Reader kept my sanity.

As for the Runners up: At lunch, Mario Kart 7 was played at my office just about daily, and when it wasn't that, it was Monster Hunter. So, those games were the really big ones for me. I also really liked the two Fire Emblems, although my favourite is still Fire Emblem 7/Blazing Sword/Advance followed by Fire Emblem 4/Genealogy of the Holy War (which I've played multiple times, including via guide in Japanese and will jump on it the moment it gets an official release...).

Radiant Historia was great as well. The game is under appreciated, IMO, and should be experienced by many more people - I hope it comes to Switch/Switch 2 in some manner. It is one of the most interestingly designed RPGs I've ever played. Although, the biggest name on the dev team is probably composer Yoko Shimomura who, if you don't know her, worked for Capcom in the 80s and 90s, and Square in the 1990s - she co-composed the Street Fighter II soundtrack, and worked on some tracks for the Square/Capcom game Breath of Fire, with Square she did Live a Live, Mario RPG (her first work with Nintendo), Parasite Eve, Kingdom Hearts, and many more (for Square, Capcom, and Nintendo). She also did tracks for Xenoblade (rejoining Mitsuda who she worked alongside with at Square), she might also be the only composer to do tracks for both Streets of Rage and Final Fight games; also both FFs, Final Fight and Final Fantasy. Her most recent project were the new arrangements for Super Mario RPG Switch.

And lastly, Rine Factory 4, it's not my favourite Rune Factory game (that was Rune Factory Frontier on Wii) but it's probably my favourite of the handheld ones - although, I'll admit, I kind of found the character art style offensive :D
So, I still liked the game in spite of not really liking the character art. It was kind of similar with a lot of RPGs around that time period, the ultra-cutesy anime style is not really to my liking. So, I just kinda... tolerated it. :D

You're darn right it is. 

Luigi's Mansion 2 HD will hopefully open the floodgates for 3DS remasters on Switch/Switch 2. It's way less effort for Nintendo to port the 3DS remakes of N64 games (despite maybe having to tweak the controls a little) than to remake the games again. Ocarina of Time is such a popular and revered game that another remake is inevitable, but it would be nice if we get the 3DS remake ported first. 

Fire Emblem Awakening

Fire emblem fates.

The Legend of Zelda: A Link Between Worlds without a doubt! Samus Returns would be second place followed by Smash.

I played brain age the most and DKC returns. I really enjoyed the pilot wings game at launch.

Most favorite would be LM Dark Moon.

I still can't believe I never played 3D world, and I'm one of the suckers who bought the system at launch. It's the only mainline Mario game I've never played.

A Link Between Worlds was the best game I played on 3DS, and I loved it.

Honorable mention to Kid Icarus.