1. Majora's Mask 3D
2. Xenoblade Chronicles 3D
3. Ocarina of Time 3D
4. Metal Gear Solid 3: Snake Eater 3D
5. Tomodachi Life

1.) Animal Crossing New Leaf
2.) Zelda ALBW
3.) Luigi's Mansion Dark Moon
4.) Tomodachi Life
5.) Super Mario 3D Land

1. Fire Emblem Awakening

2.Zero escape: Virtue's last reward

3.Animal Crossing :New Leaf

4.Persona Q

5.Steamworld Heist

(Fire emblem Fates would probably be on there but ive only finished one of the two games,and i haven't started the new Zero Time Dilema, so for now,i'll go with this)

Alright, i'll probably make the community list once the replies finally slow down.

Thank you to everyone who responded. I'd love to make this a constantly updated thread.

1. Fire Emblem Awakening
2. The Legend of Zelda: Ocarina of Time 3D
3. Kid Icarus: Uprising
4. The Legend of Zelda: A Link Between Worlds
5. Super Mario 3D Land

Currently just finished Fire Emblem Fates: Birthright, and it alone wouldn't quite crack my Top 5, but after playing the others, they or Fire Emblem Fates as a whole package may end up on the list. Working on Conquest next.

Honorable Mentions (for the heck of it, since there are SO MANY amazing 3DS games):
-Pokemon X/Y/OR/AS
-Pushmo
-Pocket Card Jockey
-Kingdom Hearts 3D: Dream Drop Distance
-Monster Hunter 4 Ultimate
-Mario Kart 7
-Fantasy Life
-Animal Crossing: New Leaf

1. The Legend of Zelda: Ocarina of Time 3D
2. Super Mario 3D Land
3. Pokémon X/Y
4. Steel Diver: Sub Wars

Dishonorable mentions:

5. Fire Emblem: Awakening
6. Mario Kart 7
7. Luigi's Mansion 2

I'm sure I'm forgetting some notable titles, which only serves to amplify how forgettable they truly were. In truth, only the top three games on my list are without glaring faults while number 4 deserves recognition for its great gameplay concept despite being free-to-play.

1. The Legend of Zelda: A Link Between Worlds
2. Pokémon X/Y
3. Mario Kart 7
4. Pokémon ΩRuby/αSapphire
5. Monster Hunter 4 Ultimate

I'll be discounting the remakes Ocarina of Time, Majora's Mask and Star Fox 64, otherwise those'd be three out of the five, the first three and in that order as well, and it's unfair imo to count old games anyway.

1. Resident Evil: Revelations
2. Luigi's Mansion 2
3. Super Mario 3D Land
4. The Legend of Zelda: A Link Between Worlds
5. Mario Kart 7

Still need to get Fire Emblem, 100% sure it would make that list.

1. Fire Emblem Fates
2. Zelda: A Link Between Worlds
3. Fire Emblem Awakening
4. Stella Glow
5. Ace Attorney 5

1. Pokemon X/Y
2. Pokemon ORAS
3. Luigi's Mansion: Dark Moon
4. Mario & Luigi Dream Team
5. Super Smash Bros 3DS