1st Party:

Pushmo

Crashmo

Dillon's Rolling Western

Dillon's Rolling Western the Last Ranger

Sakura Samurai: Art of the Sword

Ketzal's Corridors

3rd Party:

Mighty Switch Force

Mighty Switch Force 2

Mutant Mudds

Mutant Mudds 2

Johnny Kung Fu

Johnny HotShot

Johnny impossible

Touch Battle Tank 3D

Art of Balance Touch

Samurai Sword Destiny

Speed X 3D

Heavy Fire: Special Operations 3D

Denpa Men

Pix 3D

Crimson Shroud

Escape Vektor (should be $5 tops)

Gunman Clive

New game from Gunman Clive creator

Wild Adventures: Ultimate Deer Hunters 3D (you hunt a lot of non-deer animals in 3D)

Air Battle Hockey 3D

Liberation Maiden

Zen Pinball 3D (DLC is coming)

Retail that you can download:

Star Fox 64 3D

Mario Kart 7

Sonic Racing Transformed

Epic Mickey: Power of illusion

Super Mario 3D Land

Kingdom Hearts 3D

Castlevania Lords of Shadow: Mirror of Fate

New Super Mario Bros. 2

Pilotwings Resort (worth up to $15)

Paper Mario Sticker Star (RPG)

Fire Emblem: Awakening

Brain Age 3D

Sonic Racing Transformed

Bit Trip Saga (paid $10 during eShop sale)

Apps:

Netflix

Hulu Plus

MiiVerse

Swapnote

Colors! 3D (can't wait for the update)

Nintendo Video

Pokémon Dream Radar

Pokédex 3D

Pokédex 3D Pro

Ambassador Certificate

Demo:

Resident Evil: Revelations (beta graphics)

Crush 3D

Lego Batman 2

Kingdom Hearts 3D

Amazing Spider Man (felt like I was crawling on the walls & ceilings for real)

Rhythm Thief & the Emperor's Treasure

Metal Gear Solid 2 & 3 in 3D (beta graphics)

Nintendogs + cats

Mario & Sonic Full Version (but the demo of it)

Rayman Origins (the second time they put it up)

Heroes of Ruin

TheatRhythm Final Fantasy (unlimited uses)

Denpa Men

Lego Lord of the Rings

Marvel Pinball 3D

Epic Mickey Power of illusion

Adventure Time 3D

2 fast 4 Gnomz

Fire Emblem: Awakening

Brain Age 3D

Etrian Odyssey 4: Legends of the Titan

Monster Hunter 3 Ultimate 3D (it's the definitive version)

Castlevania Lords of Shadow: Mirror of Fate

Downloaded Trailers:

Mario Kart E3

Mario Kart 7 Preview

Kid Icarus: Uprising E3

Kid Icarus: Uprising Preview

Kid Icarus: Uprising Gameplay Montage

Sakura Samurai Preview

Dillon's Rolling Wetern Preview

Legend of Zelda Ocarina of time

Metal Gear Solid 2 & 3 in 3D E3 (delta graphics)

Green Lantern Movie Trailer

Star Fox E3

Animal Crossing E3

Mario Tennis preview

Paper Mario E3

Paper Mario preview

Paper Mario E3 2012

Luigi's Mansion 2 E3

Luigi's Mansion 2 preview

Luigi's Mansion Dark Moon E3

Super Mario 3D Land E3

Super Mario 3D Land Preview

Resident Evil E3

New Super Mario Bros. 2

Donkey Kong Country Returns 3D

1st Party:

Pushmo

Crashmo

Dillon's Rolling Western

Dillon's Rolling Western the Last Ranger

Sakura Samurai: Art of the Sword

Ketzal's Corridors

3rd Party:

Mighty Switch Force

Mighty Switch Force 2

Mutant Mudds

Mutant Mudds 2

Johnny Kung Fu

Johnny HotShot

Johnny impossible

Touch Battle Tank 3D

Art of Balance Touch

Samurai Sword Destiny

Speed X 3D

Heavy Fire: Special Operations 3D

Denpa Men

Pix 3D

Crimson Shroud

Escape Vektor (should be $5 tops)

Gunman Clive

New game from Gunman Clive creator

Wild Adventures: Ultimate Deer Hunters 3D (you hunt a lot of non-deer animals in 3D)

Air Battle Hockey 3D

Liberation Maiden

Zen Pinball 3D (DLC is coming)

Retail that you can download:

Star Fox 64 3D

Mario Kart 7

Sonic Racing Transformed

Epic Mickey: Power of illusion

Super Mario 3D Land

Kingdom Hearts 3D

Castlevania Lords of Shadow: Mirror of Fate

New Super Mario Bros. 2

Pilotwings Resort (worth up to $15)

Paper Mario Sticker Star (RPG)

Fire Emblem: Awakening

Brain Age 3D

Sonic Racing Transformed

Bit Trip Saga (paid $10 during eShop sale)

Apps:

Netflix

Hulu Plus

MiiVerse

Swapnote

Colors! 3D (can't wait for the update)

Nintendo Video

Pokémon Dream Radar

Pokédex 3D

Pokédex 3D Pro

Ambassador Certificate

Demo:

Resident Evil: Revelations (beta graphics)

Crush 3D

Lego Batman 2

Kingdom Hearts 3D

Amazing Spider Man (felt like I was crawling on the walls & ceilings for real)

Rhythm Thief & the Emperor's Treasure

Metal Gear Solid 2 & 3 in 3D (beta graphics)

Nintendogs + cats

Mario & Sonic Full Version (but the demo of it)

Rayman Origins (the second time they put it up)

Heroes of Ruin

TheatRhythm Final Fantasy (unlimited uses)

Denpa Men

Lego Lord of the Rings

Marvel Pinball 3D

Epic Mickey Power of illusion

Adventure Time 3D

2 fast 4 Gnomz

Fire Emblem: Awakening

Brain Age 3D

Etrian Odyssey 4: Legends of the Titan

Monster Hunter 3 Ultimate 3D (it's the definitive version)

Castlevania Lords of Shadow: Mirror of Fate

Downloaded Trailers:

Mario Kart E3

Mario Kart 7 Preview

Kid Icarus: Uprising E3

Kid Icarus: Uprising Preview

Kid Icarus: Uprising Gameplay Montage

Sakura Samurai Preview

Dillon's Rolling Wetern Preview

Legend of Zelda Ocarina of time

Metal Gear Solid 2 & 3 in 3D E3 (delta graphics)

Green Lantern Movie Trailer

Star Fox E3

Animal Crossing E3

Mario Tennis preview

Paper Mario E3

Paper Mario preview

Paper Mario E3 2012

Luigi's Mansion 2 E3

Luigi's Mansion 2 preview

Luigi's Mansion Dark Moon E3

Super Mario 3D Land E3

Super Mario 3D Land Preview

Resident Evil E3

New Super Mario Bros. 2

Donkey Kong Country Returns 3D

Dude.  You named a ton of games that aren't even out yet.  Hell, you named a bunch of games that don't even footage.  I LOVE my 3DS and I've really supported the eShop but your list is the kind of thing that has always turned me off when people had "List Wars" of the past. 

Anyway, off the top of my head from games I've actually purchased:

• Cave Story
• Zen Pinball and Marvel Pinball (darn you, SethNintendo and your awesome pinball skills!)
• Mutant Mudds (didn't like it at first but then fell in love with it!)
• Dillon's

Will edit later.  Gotta go.