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Going back to my previous point, I've decided to round up some more specific examples this gen of Nintendo's direct involvement with Japanese 3rd parties off the top of my head.  This is only stuff "above and beyond" the usual 1st party tech support, bug checks, etc, and is only inclusive of 3rd party IP (ie: no contracted work).

Square Enix

  • Children of Mana: Western publishing and promotional deals.
  • Dragon Quest Swords: Planning and co-development by Nintendo co-owned Genius Sonority
  • Heroes of Mana: Development by Nintendo owned Brownie Brown.
  • Itadaki Street DS: Mario IP lending.
  • FFCC My Life as a King: Development done with proprietary EAD tools/engine.
  • Dragon Quest Wars: Development by Nintendo owned Intelligent Systems
  • Dragon Quest IX: Western publishing and promotional deals.
  • Dragon Quest X: Western promotional deal, possibly publishing also...

SEGA

  • Mario & Sonic at the Olympic Games series: IP lending, Japanese publishing and promotional deals.
  • Rhythym Tengoku AC: IP lending.
  • Sonic in SSBB IP co-promotion.
  • Virtua Tennis 2009: European M+ bundle.
  • Sega platforms included in Virtual Console.

Capcom

  • Phoenix Wright: Ace Attourney series: European publishing and promotional deals.
  • MegaMan ZX series: European publishing and promotional deals.
  • Resident Evil DS: European publishing and promotional deals.
  • Donkey Kong Jungle Medal series: IP lending
  • Mario Party Medal series: IP lending
  • Monster Hunter G: CC bundle.
  • Monster Hunter Tri: Western publishing and promotional deals. CCPro bundles. Black Wii JP bundle.

Namco Bandai

  • Ridge Racer DS: Development by internal Nintendo studio (NST).
  • Mr Driller DS: European publishing dand promotional deals.
  • Pac-Pix/n'Roll: European publishing and promotional deals.
  • Mario Kart Arcade GP series: IP lending.
  • Super Robot Taisen OG Saga series: Development by Nintendo owned Monolith Software.
  • Tales of Graces: CC Pro and Wii JP bundles.

Level-5

  • Professor Layton series: Western publishing and promotional deals.  London Life subgame developed by Nintendo owned Brownie Brown.
  • Inazuma Eleven: Rumored western publishing and promotional deals.
  • Fantasy Life: Development by Nintendo owned Brownie Brown.

Hudson

  • PC Engine platforms included in Virtual Console
  • Various European publishing and promotional deals (Wing Island, Kororinpa series, Bomberman series, etc).
  • Sudukou Gridmaster western publishing and promotional deals.

Tecmo Koei

  • Dynasty Warriors DS: Western publishing and promotional deals.
  • Fatal Frame 4: Japanese publishing and promotional deals.
  • Samurai Warriors 3: CCPro JP bundle.  Western publishing and promotional deals.

Atlus

  • Trauma Center series: European publishing and promotional deals.
  • Etrian Odyssey series: European publishing and promotional deals.

Konami

  • Solid Snake in SSBB IP co-promotion.
  • WE Playmaker 2010: CCPro JP bundle.

Paon

  • Glory of Heracles: Worldwide publishing and promotional deals.

Marvelous Entertainment

  • Harvest Moon series: European publishing and promotional deals.
  • Lively Garden: Development by Nintendo owned Brownie Brown.

AQ Interactive / Mistwalker

  • Blue Dragon Plus: Co-development by Nintendo owned Brownie Brown.

D4 Enterprise

  • MSX and NeoGeo platforms included in Virtual Console.

Q? Entertainment

  • Meteos: Western publishing and promotional deals.

TOMY Takara

  • Naruto series: European publishing and promotional deals.

IE Institute

  • Math Training: Western publishing and promotional deals.

Chunsoft

  • Pokemon Mystery Dungeon series: Licensing and co-development deal.

FROM Software

  • Tenchu DS: Western publishing and promotional deals.

Genki

  • Lonpos: Western publishing and promotional deals.

 

...I'm sure there's many more specific instances, but those are the ones that came to me offhand.  I know there's tons more EU publishing deals too.