What 3DS games would you recommend for me?

Virtue's Last Reward. Do it.
Play 999 for DS first if you haven't. These are seriously among the best games I have ever played.

Big Kingdom Hearts fan here so if you are into/interested in them I would recommend Dream Drop Distance.

Pokemon X and/or Y Zelda OOT MGS3 no other games needed

Ocarina of Time 3D is the same game it has always been. If you want to replay it, or never played it before, I'd reccomend you buy it.

From what I have played, Shinobi was quite fun. If you liked the other games in the series, grab it, it is also relatively cheap, even for a new copy (costs about 10 euros new, where I live).

Pokemon X/Y are obvious reccomendations.

Virtue's Last Reward is quite good, as well.

Then there's Project X Zone, which I enjoyed a lot.

For eShop titles, Mighty Switch force and Pushmo/Crashmo were quite good.

Oh, and of course don't forget Monster Hunter 3 Ultimate, Kid Icarus: Uprising, Fire Emblem Awakening and Resident Evil: "Revelaitons" (yes, I have one of those copies :D).

All of these are worth your money. There are many more games worth having, for the 3DS, but these are the best ones out there. In my opinion, of course. :)

DS
Radiant Historia
Dragon Quest IV: Chapters of the Chosen
Dragon Quest V: Hand of the Heavenly Bride
Dragon Quest VI: Realms of Revelation
Dragon Quest IX: Sentinels of the Starry Skies
Shin Megami Tensei: Strange Journey
Mega Man Zero Collection
Mega Man ZX
Mega Man ZX Advent
Ghost Trick: Phantom Detective
Phoenix Wright: Ace Attorney
Phoenix Wright: Ace Attorney: Justice For All
Phoenix Wright: Ace Attorney: Trials and Tribulations
Apollo Justice: Ace Attorney
Nine Hours, Nine Persons, Nine Doors
Kirby Super Star Ultra
Kirby Canvas Curse

3DS
Etrian Odyssey IV: Legends of the Titan
Shin Megami Tensei: Devil Summoner - Soul Hackers
Shin Megami Tensei IV
Rune Factory 4
Pushmo

Monster Hunter 3 Ultimate, it lasts hundreds of hours and provides lots of fun, bonus points if you have friends with 3DS with Monster Hunter 3 Ultimate, or a WiiU with MH3U.

I have yet to play multiplayer, since I don't know anyone with the game but I just reached 200 hours of gameplay, I bought it 6 days after it came out and I still enjoy the game.

Fire Emblem: Awakening.
Pokemon X/Y.

Wait for The Legend of Zelda: A Link Between Worlds. I think it's released next month.

Animal Crossing: New Leaf

From the EShop, Steamworld Dig is an enjoyable game. It's just a sidescroller where you delve into the deeps to collect ore to get moneys for upgrades, and you find other nifty upgrades and such while down there.

Try Tales of the Abyss.