Topic: best ever 3ds eshop games.

Gunman Clive 1 & 2
Mighty Switch Force!
BoxBoy
Shovel Knight (new free DLC is almost here)
SteamWorld Dig
Inazuma Eleven is pretty good too!

VVVVVV best $8 I ever spent.

I suppose this is for 3DS eshop-only games, and it doesn't include VC or DSiWare games? Well I liked lots but my faves would have to be:

3D Classic Out Run
3D Classic Afterburner II
I Am An Air Traffic Controller Hero Hawaii
A-Train 3D City Simulator
Best of Mahjong (finally found the perfect Mahjong game after trying out several on the Eshop)

I'm gonna add another RK title to my list in Xeodrifter. Fun old school Metroid style game.

I really enjoyed Witch & Hero and Fairune - very simple 16bit styled games, that kept me engrossed until completion. They aren't big or something I'd want to play again but they were worth their small cost.

One game I expected to enjoy (and I played through to completion) was Tappingo - it was OK, but over way too quickly. IIRC it had about a hundred levels, but each could be finished very quickly and there was no difficulty scale from the first puzzle to the last. Shame. Worth skipping a cheap McDonalds meal for the purchase though if you enjoy puzzle games.

I'm gonna go for Mighty Switch Force.

Out of the ones I played:

Shovel Knight
Pushmo (Pullblox)
Nano Assault EX
Mighty Switch Force!
Cave Story
Gunman Clive

Note: I have excluded the SEGA 3D Classics that I own from the list. They are enhanced ports of classic titles.

I just picked up the physical 3ds cave story. Is the eshop version that much different and better?

It's got all the content from the + version of the game, while the 3D remake is more or less just the base game without extras.

Cave Story, Shantae's and the Pirate Curse, and Liberation Maiden will never be beaten. Not even Shovel Knight come close to the games I listed.

To add to @Morpheel, CS3D likes to lag a lot. It's also pretty hard to tell platforms from the background.

My favorite eShop games (in order) are:

5. Retro City Rampage DX
4. Cave Story (despite being sick of the game itself)
3. VVVVVV
2. Picross (any)
1. Crimson Shroud

HarmoKnight
Shovel Knight
Cave Story
Liberation Maiden

Those are among my favorites on the eShop.

Cave Story
VVVVVV
HarmoKnight
Shovel Knight

Cave Story, hands down my favorite so far on the 3Ds eShop so far.
Also got Phoenix Wright: Ace Attorney: Dual Destinies and it's pretty cool so far. c:

It's significantly cheaper!

I like all Those myself I would love to add to this list:
Crimson Shroud
Attack of the Friday Monsters and
Inazuma Eleven
All very good games along with the ones listed above

The Air Traffic Control game really is awesome! I highly recommend that to anyone. very neat Airport simulator. give this game some love and buy it! its on sale for 9.99 every once in while. get it then its worth every penny.

I have to many I love to Narrow it down to 1 favorite game. there are so many good ones. most memorable for me would be Crimson Shroud. what a cool story. I also like Shovel Knight Quite a bit. the Eshop has changed so much the last couple of years and has become the real deal of good games.