This'll be a fairly big read and I'm going to set out the same information in different ways to get a few different perspectives on it all. I'll add a team by team list in the second post.
Below is a year by year list of what games the many teams inside of nintendo have released.
KEY
EAD1
EAD2
EAD3
EAD4
EAD5
EAD Tokyo
SPD = Software Planning and Development
SDD = Nintendo Software Design and Development
NSD = Nintendo Network Service Development
NST = Nintendo Software Technology
2003
IN HOUSE
- EAD1 - Mario Kart Double Dash!!
- EAD3 - The Legend of Zelda: The Wind Waker
- EAD4 - Super Mario Advance 4: Super Mario Bros. 3
- Brownie Brown - Sword of Mana
- Intelligent Systems - WarioWare Inc.: Mega Party Games (GCN Remake)
- Intelligent Systems - Nintendo Puzzle collection
- NST - 1080 Avalanche
- NST - The Legend of Zelda: Collector's Edition
- Ambrella - Pokemon Channel
- Camelot - Golden Sun: The Lost Age
- Camelot - Mario Golf: Toadstool Tour
- Genius Sonorit - Pokemon Colleseum
- HAL Laboratory - Kirby Air Ride
- Nd Cube - Tube Slider
- Skip Ltd. - GiFTPiA
- Suzak - F-Zero: GP Legend
- EAD1 - Pikmin 2
- EAD3 - The Legend of Zelda: Four Swords Adventure
- EAD4 - Super Mario 64 DS
- EAD4 - Band Brothers
- EAD Tokyo 1 - Donkey Kong: Jungle Beat
- SDD - Daigasso! Band Brothers
- SPD 1 - WarioWare: Touched!
- SPD 1 - WarioWare Twisted!
- SPD 3 - Metroid Prime 2: Echoes
- Intelligent Systems - Paper Mario: The Thousand Year Door
- Intelligent Systems - WarioWare: Touched!
- Intelligent systems - WarioWare: Twisted!
- NST - Mario vs. Donkey Kong
- NST - Ridge Racer DS
- Retro Studios - Metroid Prime 2: Echoes
- Ambrella - Pokemon Dash
- Camelot - Mario Golf: Advance Tour
- Camelot - Mario Power Tennis
- Game Freak - Pokemon FireRed and LeafGreen
- HAL Laboratory - Kirby and the Amazing Mirror
- Noise - Custom Robo
- Suzak - F-Zero: Climax
- EAD1 - Nintendogs: Duchshund and Friends
- EAD1 - Nintendogs: Lab and Friends
- EAD1 - Nintendogs: Chihuahua and Friends
- EAD1 - Nintendogs: Best Friends Version
- EAD2 - Animal Crossing: Wild World
- EAD4 - Big Brain Academy
- EAD4 - Yoshi Touch and Go
- SDD - Brain Age: Train Your Brain in Minutes a Day!
- SDD - Brain Age 2: More Training in Minutes a Day!
- SPD 2 - Super Princess Peach
- SPD 2 - Mahjong DS
- SPD 3 - Battalion Wars
- SPD 3 - Geist
- Intelligent Systems - Fire Emblem: Path of Radiance
- Intelligent Systems - Advance Wars: Dual Strike
- Agenda - Clubhouse Games
- AlphaDream - Mario and Luigi: Partners in Time
- Camelot - Mario Tennis: Power Tour
- Cing - Another Code: Two Memories
- Creatures Inc. - PokePark: Fishing Rally DS
- Game Freak - Pokemon Emerald
- Game Freak - Drill Dozer
- Genius Sonority - Pokemon XD: Gale of Darkness
- HAL Laboratory - Kirby: Canvas Curse
- Indieszero - Electroplankton
- Indieszero - Sennen Kazoku
- Kuju Entertainment (Headstrong Games) - Battalion Wars
- Next Level Games - Super Mario Strikers
- Paon - DK: King of Swing
- Skip Ltd. - Chibi-Robo
- TOSE - Super Princess Peach
- EAD1 - Mario Kart DS
- EAD1 - Nintendogs: Dalmation and Friends
- EAD2 - Wii Sports
- EAD2 - Wii Play
- EAD2 w/ Q-Games - Star Fox Command
- EAD3 - The Legend of Zelda: Twilight Princess
- EAD4 - New Super Mario Bros.
- SDD - DS Easy Dictionary
- SDD - DS Dhigureden
- SDD English Training: Have Fun Improving Your Skills!
- SPD 1 - WarioWare: Smooth Moves
- SPD 1 - Rhythm Tengoku
- SPD 2 - Tetris DS
- SPD 3 - Excite Truck
- SPD 3 - Mother 3
- SPD 4 - Wii Menu Channels
- Brownie Brown - Magical Starsign
- Brownie Brown - Mother 3
- Intelligent Systems - WarioWare: Smooth Moves
- NST - Metroid Prime Hunters
- NST - Mario vs. Donkey Kong: March of the Minis
- Artoon - Yoshi's Island DS
- Game Freak - Pokemon Diamond and Pearl
- Genius Sonority - Pokemon Trozei!
- HAL Laboratory - Mother 3
- HAL Laboratory - Kirby Squeak Squad
- HAL Laboratory - Pokemon Ranger
- Indieszero - It Talks! DS Cooking Navigator
- Monster Games - Excite Truck
- Noise - Custom Robo Arena
- Skip Ltd. - bit Generations Series One
- Skip Ltd. - bit Generations Series Two
- EAD3 - The Legend of Zelda: Phantom Hourglass
- EAD3 - Link's Crossbow Training
- EAD4 - Big Brain Academy
- EAD5 - Wii Fit
- EAD Tokyo 1 - Super Mario Galaxy
- SPD 1 - Light Speed Card Battle: Card Hero
- SPD 2 - Planet Puzzle League
- SPD 3 - Battalion Wars 2
- SPD 3 - Metroid Prime 3: Corruption
- SPD 4 - Everybody Votes Channel
- SPD 4 - Mii Contest Channel
- NSD - Slide Adventure: MAGKID
- Brownie Brown - Heroes of Mana
- Intelligent Systems - Fire Emblem: Radiant Dawn
- Intelligent Systems - Super Paper Mario
- Intelligent Systems - Light Speed Card Battle: Card Hero
- Intelligent Systems - Planet Puzzle League
- Retro Studios - Metroid Prime 3: Corruption
- Agenda - Slide Adventure: MAGKID
- Arika - Endless Ocean
- Camelot - We Love Golf!
- Cing - Hotel Dusk: Room 215
- Genius Sonority - Pokemon Battle Revolution
- Genius Sonority - 100 Classic Book Collection
- Kuju Entertainment (Headstrong Games) - Battalion Wars 2
- Mistwalker - ASH: Archaic Sealed Heat
- Next Level Games - Mario Strikers Charged Football
- Paon - DK: Jungle Climber
- Paon - Donkey Kong Barrel Blast
- Racjin - ASH: Archaic Sealed Heat
- Skip Ltd. - Chibi-Robo!: Park Patrol
- Skip Ltd. - LOL (Archime DS)
- Suzak - Wario: Master of Disguise
- EAD1 - Mario Kart Wii
- EAD1 - Nintendo DSi Sound
- EAD2 - Animal Crossing: Let's Go to the City
- EAD2 - Wii Music
- EAD4 - Band Brothers DX
- EAD4 - NPC! Pikmin
- EAD Tokyo 2 - NPC! Donkey Kong Jungle Beat
- EAD Tokyo 2 - Flipnote Studio
- SDD - Daigasso! Band Brothers DX
- SDD - Brain Age Express: Arts and Letters
- SDD - Brain Age Express: Math
- SDD - Brain Age Express: Sudoku
- SPD 1 - Rhythm Heaven
- SPD 1 - Paper Planes
- SPD 1 - Birds and Beans
- SPD 2 - Style Savvy
- SPD 2 - Dr. Mario Online Rx
- SPD 2 - A Little Dr. Mario
- SPD 2 - A Little Magic Collection
- SPD 2 - Chotto Asobi Taizen: Otegaru Trump
- SPD 4 - Nintendo Channel
- SPD 4 - Digicam Print Channel
- SPD 4 - Fortune Telling Channel
- SPD 4 - DSi Browser
- NSD - Super Smash Bros. Brawl
- NSD - Personal Trainer: Walking
- NSD - Cooking Guide: Can't Decide What to Eat?
- Brownie Brown - Blue Dragon Plus
- Intelligent Systems - Advance Wars: Days of Ruin
- Intelligent Systems - Fire Emblem: Shadow Dragon
- Monolith Soft - Disaster: Day of Crisis
- Monolith Soft - Super Smash Bros. Brawl
- Monolith Soft - Soma Bringer
- NST - Crosswords DS
- Ambrella - My Pokemon Ranch
- Arika - Dr. Mario Express
- Arika - Dr. Mario Online RX
- Artoon - The World of Golden Eggs: Nori Nori Rhythm-Kei (Wii)
- Creatures Inc. - Personal Trainer: Walking
- Creatures Inc. - Pokemon Ranger: Shadows of Almia
- Creatures Inc. - Project Hacker
- Game Freak - Pokemon Platinum
- Good-Feel, Inc - Wario Land: The Shake Dimension
- HAL Laboratory - Kirby Super Star Ultra
- HAL Laboratory - Super Smash Bros. Brawl
- Indieszero - Cooking Guide: Can't Decide What to Eat?
- Paon - Glory or Heracles
- Skip Ltd. - Captain Rainbow
- Skip Ltd. - Art Style: ORBIENT
- Skip Ltd. - Art Style: CUBELLO
- Skip Ltd. - Art Style: ROTOHEX
- Skip Ltd. - Art Style: Aquia/Aquite
- Skip Ltd. - Art Style: Code/Base 10
- Sora - Super Smash Bros. Brawl
- Syn Sophia - Style Savvy
2009
- EAD2 - Wii Sports Resort
- EAD3 - The Legend of Zelda: Spirit Tracks
- EAD4 - NPC! Pikmin 2
- EAD4 - New Super Mario Bros. Wii
- EAD5 - Wii Fit Plus
- SPD 1 - WarioWare: Snapped!
- SPD 1 - WarioWare: DIY
- SPD 1 - WarioWare: DIY Showcase
- SPD 1 - Friend Collection
- SPD 2 - Sin and Punishment 2
- SPD 2 - Clubhouse Games Express: Card Classics
- SPD 2 - Chotto Asobi Taizen: Onajimi Table
- SPD 2 - Clubhouse Games Express: Family Favorites
- SPD 2 - Clubhouse Games Express: Strategy Pack
- SPD 3 - Punch-Out!!
- SPD 3 - ExciteBots: Trick Racing
- SPD 3 - Excite Bike: World Rally
- SPD 3 - Mario vs Donkey Kong: Mini's March Again
- SPD 4 - Delivery Channel
- HAL Laboratory - Picross 3D
- Intelligent Systems - WarioWare: Snapped!
- Intelligent Systems - WarioWare: DIY
- Intelligent Systems - Dragon Quest
- Intelligent Systems - Eco Shooter: Plant 530
- Intelligent Systems - Panel Connection: 3 Minute Rocket
- NST - Mario vs Donkey Kong: Mini's March Again
- NST - Mario Clock and Calculator
- NST - Animal Crossing Clock and Calculator
- NST - Aura-Aura Climber
- Retro Studios - Metroid Prime Trilogy
- AlphaDream - Mario & Luigi: Bowser's Inside Story
- Ambrella - PokePark Wii Pikachus's Great Adventure
- Ambrella - Pokemon Rumble
- Arika - Endless Ocean 2
- Arika - Aa Majou Setsuna (Coming to the West in 2010 as Metal Torrent)
- Artoon - The World of Golden Eggs: Nori Nori Rhythm-Kei (DS)
- Brownie Brown - Kappa Michi
- Camelot - New Play Control: Mario Power Tennis
- Cing - Another Code: R - A Journey into Lost Memories
- Creatures Inc. - PokePark Wii Pikachu's Great Adventure
- Creatures Inc. - Spin Six/Kuru Kuru Action Kuru Pachi 6
- Creatures Inc. - Pokemon Heart Gold/Soul Silver
- Game Freak - Pokemon Heart Gold/Soul Silver
- HAL Laboratory - Picross 3D
- Monster Games - ExciteBots: Trick Racing
- Monster Games - Excite Bike: World Rally
- Next Level Games - Punch-Out!!
- Next Level Games - Jungle Speed
- Noise - Go Go Cosmo Cops
- Q-Games - Trajectile
- Q-Games - Starship Defence
- Skip Ltd. - Art Style: Boxlife
- Skip Ltd. - Art Style: Kubos/Precipice
- Skip Ltd. - Art Style: Picopict/Pictobits
- Skip Ltd. - Art Style: Nemrem/Zengage
- Skip Ltd. - Art Style: Intersect/Digidrive
- Skip Ltd. - New Play Control: Chibi-Robo
- Skip Ltd. - Okaeri! Chibi-Robo! Happy Richie Osoji!
- SRD Co. - Photo Dojo
- Treasure - Sin and Punishment 2
- EAD Tokyo 1 - Jibun de Tsukubu Nintendo DS Guide
- EAD Tokyo 2 - Super Mario Galaxy 2
- SPD 1 - Metroid: Other M
- SPD 2 - Metal Torrent
- SPD 2 - Endless Ocean 2: Blue World
- SPD 2 - Xenoblade Chronicles
- SPD 3 - Donkey Kong Country Returns
- SPD 4 - Wii Party
- SPD 4 - Mario Sports Mix
- Brownie Brown - Livly Garden
- Intelligent Systems - Fire Emblem Remake DS
- NST - Mario vs. Donkey Kong: Mini-Land Mayhem
- Monolith Soft - Xenoblade Chronicles
- Project SORA - Kirby's Epic Yarn
- Retro Studios - Donkey Kong Country Returns
- AQ Interactive - The Last Story
- Artoon - Fling Smash
- Camelot - Golden Sun: Dark Dawn
- Cing - Last Window: The Secret of Cape West (Cing filed for Bankruptcy in March 2010)
- Creatures Inc. - Pokemon Ranger: Path of Light/Guardian Signs
- Creatures Inc. - Pokemon Black/White
- Game Freak - Pokemon Black/White
- Grezzo - Line Attack Heroes
- Good-Feel, Inc - Looksley's Line Up
- Good-Feel, Inc - Kirby's Epic Yarn
- Mistwalker - The Last Story
- Nd Cube - Wii Party
- Noise - ArcoKnights
- Project M - Metroid: Other M
- Q-Games - 3D Space Tank/X-Scape
- Shift - Ando Kensaku
- Skip Ltd. - Art Style: Light Trax
- Skip Ltd. - Art Style: Rotozoa
- Skip Ltd. - Snowpack Park
- Square Enix - Mario Sports Mix
- EAD1 - Nintendogs & Cats
- EAD1 - Mario Kart 3DS
- EAD3 - The Legend of Zelda: Skyward Sword
- EAD5 - Steel Diver
- EAD Tokyo 1 - Super Mario 3DS
- CSDG - Starfox 64 3D
- SDD - Nintendo 3DS OS, GUI
- SPD 1 - Rhythm Heaven Fever
- SPD 2 - Wii Play: Motion
- SPD 3 - Pilotwings Resort
- Brownie Brown - Super Mario 3D Land
- Creatures Inc. - Pokepark 2: Wonders Beyond
- Monolith Soft - The Legend of Zelda: Skyward Sword
- HAL Laboratory - Face Raiders
- HAL Laboratory - Kirby's Return to Dream Land
- HAL Laboratory - Kirby Mass Attack
- Intelligent Systems - Pushmo/Pullblox
- Project SORA - Kid Icarus: Uprising
- Retro Studios - Mario Kart 7
- Ambrella - Pokemon Rumble Blast
- Arika - 3D Classics Excitebike
- Arika - 3D Classics Xevious
- Arika - 3D Classics Urban Championship
- Arika - 3D Classics Twinbee
- Arika - 3D Classics Kirby's Adventure
- Arzest - Wii Play Motion
- Big Fish Games - Mystery Case Files: Dust to Dust
- Chunsoft - Wii Play Motion
- Gambarion - Pandora's Tower
- Grezzo - The Legend of Zelda: Ocarina of Time 3D
- Grezzo - The Legend of Zelda: Four Swords Anniversary
- Genius Sonority - Battle & Get! Pokemon Typing DS
- Mitchell Corporation - Wii Play Motion
- Monster Games - Pilotwings Resort
- Nd Cube - Wii Play Motion
- Prope - Wii Play Motion
- Skip Ltd. - Wii Play Motion
- Vanpool Inc. - Wii Play Motion
- Vetei Inc. - Steel Diver
2012
- EAD2 - Animal Crossing 3DS
- EAD2 - Nintendo Land
- EAD4 - New Super Mario Bros. 2
- EAD4 - New Super Mario Bros. U
- EAD4 - Pikmin 3
- EAD5 - Wii U Fit
- SPD 1 - Game & Wario
- SPD 1 - Kiki Trick
- SPD 1 - Friend Collection 2
- SPD 4 - Mario Party 9
- UNKNOWN - Wii U Panorama
- Brownie Brown - Fantasy Life 3DS
- Intelligent Systems - Paper Mario 3DS
- Intelligent Systems - Fire Emblem: Awakening
- Alpha Dream - Unannounced 3DS Title?
- Arika - 3D Classics Kid Icarus
- Camelot - Mario Tennis 3DS
- Creatures Inc. - Pokemon Grey
- Game Freak - Pokemon Grey
- Genius Sonority - Denpa Ningen
- Nd Cube - Mario Party 9
- Next Level Games - Luigi's Mansion 2
- Syn Sophia - Style Savvy 3DS
2013
- EAD2 - Wii Sports U
- EAD3 - The Legend of Zelda 3DS
- EAD Tokyo 2 - Super Mario Wii U
- Monolith Soft - Unanounced 3DS Title
- Retro Studios - Unannounced Wii U title
- Creatures Inc. - Pokemon 3DS
- Game Freak - Pokemon 3DS
- EAD1 - Mario Kart Wii U
- EAD2 - Animal Crossing Wii U
- EAD3 - The Legend of Zelda Wii U
- Monolith Soft - Unanounced Wii U Title
- Project SORA - Super Smash Bros. 3DS
- Project SORA - Super Smash Bros. Wii U