There are a lot of really good ones suggested on this thread. I think that if I based my favorite 3DS game based on time invested then it'd be Rune Factory 4. It's strange that I liked this game so much because i couldn't stand Harvest Moon (the flagship series.) I think that the combat maybe breaks up the monotony of farming for hours on end.

Beyond that, I really like Etrian Odyssey Untold: Millennium Girl. I really like the map drawing element of it. I think that it's a nice diversion from usual JRPG fare. Creating your own party also allows for a lot of flexibility.

CthulWho : That's really cool, nice uncommon choices. I haven't heard of either but I might look into them.

My favorite 3DS game at the moment is Pokémon Omega Ruby. I think they are wonderful remakes and I can't wait for my favorite generation to get remakes...generation 4. Although, they probably won't be on 3DS...

Okay. Here's my list. 

So first of all, let's mention how ecstatic I was when they came out with both Ocarina of Time and Majora's Mask for 3DS. Both were games I'd fallen in love with in my childhood, and I'd been dying to play them again. Oh, and Link Between Worlds is pretty fun too, but I have a soft spot for the N64 classics.

Second, let's talk about Pokémon. Pokémon X/Y were really good when I played them, but I've got to admit - what they did with ORAS was uh-MAZING. I played through that sucker in three days, and was blown away every step of the way.

Next I'd like to commend Fire Emblem: Awakening. I had never really played the Fire Emblem titles for GBA, but I'm sure this one beats them all. Epic storyline, well-developed characters, awesome graphics - overall wow.

And Mario Kart 7 is hella fun to do when I get tired of RPG's. Lol.

Besides that, I also really enjoy the other sorts of games available, like Pokémon Art Academy and Brain Age: Concentration Training. Art Academy is just super fun and relaxing to do, and the current Brain Age title has really taken it up a notch. That's about it

Super Smash Bros for Nintendo 3DS. I absolutely LOVE that game. I do like the Wii U version better though, but I digress.

Ok, I had my 3DS for a little while since my last post (almost a year). So far, I already got a total of 13 games (which is an increase of 8 games since my last post with 5 games). So, for my favorite game so far has to be Super Smash Bros, because come on, it's Smash Bros. on a handheld, you can't get wrong with that.

LunarDarkness2 : Don't be too sure, each Pokemon Generation goes into a new Handheld (I - GB, II - GBC, III - GBA, IV - DS, V - DSi, VI - 3DS, so, VII will be on the New 3DS [or N3DS]), so, you may see a Sinnoh remake on the New 3DS.

IgorBird122 : I highly doubt that Gamefreak would make gen VII exclusively on the New 3DS because there are plenty of people out there who haven't bought the new model and won't want to have to spend a lot of money on the New 3DS.. When they finally do make Gen VII games, I'd either expect them to be on all 3DS models or a less likely scenerio being that they'd be on Nintendo's next gen handheld.

FIRE EMBLEM AWAKENING.
This game is amazing, and I've played some truly great 3DS games. All the main Pokemon games, and Monster Hunter 4 Ultimate.
It's typical Fire Emblem norm. Strategic battles. Don't like the fact that you can grind and reclass? I personally like those things, and I loved both Blazing Sword and Radiant Dawn. You can play it like those two games if you want. Awakening is a step in the right direction, and I'd like to see what they do with Fire Emblem 14.

Ooh, that's a really tough question for me to answer... I'm torn between Pokémon Alpha Sapphire and Animal Crossing: New Leaf. I'm practically done with Alpha Sapphire forever now, so I guess I'll go with New Leaf.
As for eShop exclusives, Mutant Mudds in #1 and VVVVVV is a close second. Sorry, BOXBOY!, you're in third place.

gamerforlifeforever2 : My guess is that Nintendo would release it for the normal 3DS, because my guess is that the New 3DS will only have 1 or 2 exclusive games (Xenoblade Chronicles) and the rest will all be universally compatible. It'll be like the DSi. The same system with a few new cool features, but you don't really need it to play the system's actual games.

Pokemon omega ruby/Alpha sapphire. The rest seemed tedious. SSB4 was kinda of a disappointment to me. That trailer really deceived me. Perhaps I overestimated it...

Monster Hunter 4 for me its a great game

I'm a bit behind the times when it comes to 3DS games, meaning I haven't bought one in three years.

Therefore my favourite 3DS game is either Mario Kart 7 or Street Fighter IV. Both are highly competent games, and they're fun to play regardless of their age.

taterii : I think it's Super Mario 3D Land for the 3DS. I mean it kinda combines the aspects of Super Mario Bros. 3 and a regular 3D Mario game. It has quite good content in it and has Streetpass features as well. It has interesting levels and maybe some rage quiting levels as well. The graphics are at least decent and the addictiveness are okay too.
   I would've pick Fire Emblem Awakening but I don't have that game though.

Pokemon X/Y or Super Monkey Ball 3D. Both are great games and I recommend anyone to try them. SMB 3D is a bit childish and more for younger audiences, but I still play it. 

Boxia : I know your on a posting spree and such trying to get a jersey or two. But I just wanted to point out that Mario Kart 8 is only for the Wii U not the 3DS. Mario kart 7 is the game that you were talking about.

I haven't played many 3DS titles but I would have to say Xenoblade Chronicles 3D is my favorite game. Super Smash Bros. 4 being a close second.

I just got my 2DS recently, so I only have 3 games. LoZ: Link Between Worlds, Mario Kart 7, and Monster Hunter 4 Ultimate. I haven;t even touched Zelda, even though I really, really want to, and I got kind of bored of MK7. So, Monster Hunter 4 Ultimate. When my friend bought the game for me, he apologized and told me it was a huge time sink... He was right... I keep playing that thing, even though I really want to try the Zelda game... But no matter how many missions you do, and monsters you hunt, there are always more.

   My favorite part has to be the fact that whatever you kill, you can wear, or make weapons out of... It's so incredibly cool. I've got a whole Najarala set (minus the head, that Chilling Beak is just too annoyingly rare!), because I love the Aztec feel of it. Even though my ice resistance is about -18 because of it. XD

Although I've liked several games a lot so far, my two Favorites up to this point are "A Link Between Worlds" and the "Majoras Mask 3D" remake. Both are great titles for Zelda fans. I highly recommend checking them out.

taterii : Mines is pokemon omega ruby. The remake brought back so much memories. Nostalgic .

taterii : my favorite 3ds game , as well as possibly my favorite game of all time, is Kid Icarus Uprising, I love every single thing about it, (except for Hades Heart) the music. Amazing. The game play. Amazing. EVEN THE VOICE ACTING'S GREAT ( Hades is like my video game be)