Fantasy Life was a fun boredom killer for me.
Kid Icarus: Uprising was lots of fun.
Tales of the Abyss is good, long RPG.
Hmm, Xenoblade Chronicles is another long RPG.
Fire Emblem: Awakening, Luigi's Mansion: Dark Moon, Mario & Luigi: Dream Team, Pushmo, Super Mario 3D Land, Pokemon, Ocarina 3DS, Majora's Mask 3DS, Shovel Knight, Monster Hunter 4 Ultimate, Resident Evil: Revelations, Kirby: Triple Deluxe, um..

Well, these are ones I have personally liked.

Note that Xenoblade Chronicles isn't a 3DS game, it's a New 3DS Game.

Etrian Mystery Dungeon is quite good, as is Lego City Undercover: THe Chase Begins, Animal Crossing, the other Etrian Odyssey games, Skylanders Swap Force (if you already have some Skylanders. Note the other Skylanders 3DS games kinda suck.), Mario Kart 7, Crimson Shroud is a very good very old-school RPG,.

And it's DS, not 3DS, but Solatorobo: Red the Hunter is lots of fun. It's a sort-of sequel to the Playstation game 'Tail Concerto'.

Oh yea, I forgot that fact about Xenoblade, whoops.

MH4U the only time stealer you will need lol

monster hunter. I played the SMB 2 coin one, its ok. I havent played alot

monster hunter 4 ultimate, Etrian odyssey series,

Etrian Mystery Dungeon was a great one to pick up! It's not quite like the other Etrian Odyssey games, which are more traditional dungeon-crawls and also really good. I also liked Harvest Moon A New Beginning, if you're into that sort of thing.

Monster Hunter 4 Ultimate is, of course, one of the pinnacle 3DS games, even if it seems to be of a niche audience.

Luigi's Mansion: Dark Moon is also a great one worth picking up.

Rune Factory 4 is like Harvest Moon, except for a broader audience thanks to the Zelda-like dungeon elements, making it even better, arguably!

You can try Super Smash bros if you wanna :)

Senran Kagura: Burst is pretty fun. a downloadable title(I think) which is done in the same vein as side scroller beat 'em ups with Busty Ninja girls.

Yeah sent an is a funew game. I know in the jap vers in the dlc there is a boob slider. I would like to show you the game from the ps4. Not the same but I think you would enjoy the characters. The main thing you should know about the game. The more times you get hit. The more your cloths gets shredded off. And yes this is a 3ds game

Didn't know there was going to be a PS4 Senran Kagura game. I know about the Vita but didn't know there was a PS4 game.

yeah its right now jap only. but who knows. i do know you can get banned on twitch for streaming the ps4 game

Hmm, I see.

Rune Factory 4

Azure Striker Gunvolt. It's a side-scrolling action game by the company that made the Mega Man Zero series.

Well, if you like Zelda, you can't go wrong with Majora's Mask 3D. If you enjoy Smash, Super Smash Bros is great (I played it on every bus ride to and from work, and occasionally during lunch). Shovel Knight is pretty fantastic if you enjoy old-type platformers (it's REALLY solid). I found Kid Icarus Uprising very enjoyable, but other people complain about the uncomfortableness of holding the 3DS with one hand and the stylus in the other at all times (I only ever played it while lying on my bed so I never experienced that, maybe it depends on your seating conditions); though it's a game where you'll want the volume on at all times, so I guess that also depends on where you are for lunch break? Fire Emblem Awakening is an option if you like strategy, though if you're the analytical/cautious type like me, maps could take longer than a single lunch break >.>

Also consider downloading some demos from the eShop and seeing if any of those strike your fancy!

Oh, and Shin Megami Tensei IV if you're into Atlus RPGs at all.

Since I kind of skimmed through the comments already posted:
Pokemon X/Y
Yokai Watch
Dragon Quest(any of them really, but IX is original for the DS)
Chrono Trigger
LBX
Fantasy Life
Monster Hunter Generations(or Monster Hunter 4 Ultimate)
The Phoenix Wright Trilogy
Phoenix Wright: Dual Destinies
Etrian Odyssey(the remakes that just came out are good)
Now, these are ones I've played and enjoyed.