Might as well add this, too. For all intents and purposes, they're Nintendo "developers". (NB: I started but haven't finish noting who published these.)
FRIENDLY THIRD PARTY (close ties with Nintendo, often published or distributed by Nintendo) (significant/recent releases listed only)
Treasure
Alien Soldier, Sega MegaDrive (1995)
Sin and Punishment, N64 (2000) *with Nintendo R&D
Ikaruga, Dreamcast & GCN (2001) *with G.rev
[...]
Advance Guardian Heroes, GBA (2004)
Gunstar Super Heroes, GBA (2005)
Bleach: The Blade of Fate, DS (2006)
Bleach: Dark Souls, DS (2007)
Bangai-O Spirits, DS (2008)
Sin & Punishment: Star Successor, Wii (October 2009) *with SPD2
3 Xbox Live Arcade ports/upgrades (Bangai-O HD: Missile Fury, Radiant Silvergun, Guardian Heroes) (May-October 2011)
Untitled 3DS Action Game
???
By E3 2013, Treasure will have been working on their next game(s) for over three years, which is striking considering the regularity of their past output. The CEO in November revealed they're working on a 3DS action game, but I wouldn't be surprised if they've been working on something else too. Possibly Wii U, but too early in development to comment about. Expect a 3DS reveal by June, maybe Sin & Punishment 3DS.
Arika
Endless Ocean, Wii (2007) *with SPD2
Dr. Mario Online Rx, WiiWare (2008)
Dr. Mario Express, DSiWare (2008)
Endless Ocean 2: Blue World (2009) *with SPD2
3D Classics (Series 1: ExciteBike & Xevious), 3DS eShop (throughout 2011)
Bust-A-Move Universe, 3DS (2011) [pub. by Square Enix]
Tekken 3D: Prime Edition, 3DS (February 2012) *with Namco Bandai [pub. Namco Bandai]
???
Hopefully 3D Classics Series 2 (it may be more feasible now that 3DS has taken off in Japan), but as for now the official word is that there won't be any more. In June 2011, stereoscopic 3DS images of a Street Fighter EX test project (called "Fighting Sample") were revealed, but the VP of Arika tweeted that this was for mobile development. It seems to have taken them a while! Maybe it's been switched to 3DS. The likely alternative is another Endless Ocean, but I don't see how that would be given a priority.
Artoon
Yoshi Topsy-Turvy, GBA (2004)
[…]
Yoshi's Island DS, DS (2006)
Blue Dragon, 360 (2006) *with Mistwalker
Vampire Rain: Altered Species, 360 & PS3 (2007-2008)
Away: Shuffle Dungeon, DS (2008) *with Mistwalker [pub. AQ Interactive]
The World of Golden Eggs, Wii & DS (2008-2009) [pub. AQ Interactive]
Echoshift, PSP (2009)
Club Penguin: Game Day! (2010) *published by Disney
FlingSmash, Wii (2010)
Robotics;Notes (graphical novel), PS3 & 360 (June 2012) *with 5pb.
???
Artoon has little to show for itself since 2010, and I wonder whether it's fallen out of favour with Nintendo due to some poorly received titles. I'm listing them just in case, because they could have been working on a major new Nintendo IP title over the last 2 years.
Mistwalker (all releases listed)
Blue Dragon, 360 (2006) *with Artoon
Lost Odyssey, 360 (2007) *with feelplus
ASH: Archaic Sealed Heat, DS (2007) *with Racjin
Blue Dragon Plus, DS (2008) *with Brownie Brown & feelplus [pub. AQ Interactive]
Away: Shuffle Dungeon, DS (2008) *with Artoon [pub. AQ Interactive]
Blue Dragon: Awakened Shadow, DS (2009-2010) *with tri-Crescendo, Bird Studio & Namco Bandai
The Last Story, Wii (January 2011) *with AQ Interactive [pub. NINTENDO & XSeed]
Party Wave & Blade Guardian, iOS (2012)
???
Based in Tokyo and Hawaii, founded and originally financially backed by Microsoft in 2004, Mistwalker (who focuses on story and music, outsourcing development to others like feelplus or Artoon for a pretty fast turnaround) soon switched to focus on Nintendo platforms (apart from some minor games on iOS through mid 2012). At E3 2012, the developers announced they are excited to work on a Wii U action-RPG but hadn't really planned anything yet. We may get a tease later in 2013 for a Japanese release.
Headstrong Games (division of Kuju Entertainment) (all releases listed)
Battalion Wars 2, Wii (2007) *with SPD3 [pub. NINTENDO]
The House of the Dead: Overkill, Wii (2009) [pub. Sega]
Art Academy (First & Second Semesters), DSiWare & DS (2009-2010) *with SPD3 [pub. NINTENDO]
The Sorcerer's Apprentice, DS (2010)
The Lord of the Rings: Aragorn's Quest, Wii (2010)
The House of the Dead: Overkill: Extended Cut, PS3 (2011)
Silent Hill: Downpour, PS3 & 360 (2012) *with Vatra
Top Gun: Hard Lock, PS3 & 360 (2012)
Rabbids Rumble, 3DS (November 2012) [pub. Ubisoft]
New Art Academy, 3DS (July 2012, DLC through 2013) *with SPD3 [pub. NINTENDO]
???
Headstrong, based in London, is probably one of the most eclectic developers (mostly quick, mediocre tie-ins), and specialises in working with Nintendo (the other branches of Kuju Entertainment do the opposite). They have a quick turnaround but I don't imagine anything significant (like Art Academy Wii U or Battalion Wars 3) making 2013.
Vanpool
Freshly-Picked Tingle's Rosy Rupeeland, DS (2006)
Ripening Tingle's Balloon Trip of Love, DS (2009)
Wii Play: Motion (one racing mini-game only), Wii (2011) *with SPD1
Dillon's Rolling Western, 3DS eShop (2011)
???
At the time of release, a sequel to Dillon's Rolling Western (originally "The Rolling Western") was obviously planned (hinted in the secret ending), and Nintendo's boasting about the unique game and its name-change suggests they are committed to establishing and evolving this new character and IP (possibly an appearance in Smash, too?). By E3 2013, Vanpool will have worked on something for at least 2 years, so maybe it'll be a fully fledged retail Dillon (more of an adventure like the Tingle series?).
PlatinumGames (formerly Clover Studio) (all releases listed)
MadWorld, Wii (2009) [pub. Sega]
Infinite Space, DS (2009) *with Nude Maker [pub. Sega]
Bayonetta, PS3 & 360 (2009) [pub. Sega]
Vanquish, PS3 & 360 (2010) *with Straight [pub. Sega]
Anarchy Reigns, PS3 & 360 (2012) [pub. Sega]
The Wonderful 101, Wii U (Q1 2013) [pub. NINTENDO]
Metal Gear Rising: Revengeance, PS3 & 360 (TBA 2013) [pub. KONAMI]
Bayonetta 2, Wii U (TBA 2013-2014) [pub. NINTENDO]
???
Although noted for a fast and relatively quality turnaround, Platinum has their plate full throughout 2013; we may get a trailer for Bayonetta at E3, but not much else. For the record, Platinum is comprised of employees of the now defunct Clover Studio (a Capcom funded enterprise), whose output was the Viewtiful Joe series (GCN and PS2), and Okami and God Hand (both PS2), but all those IPs remain property of Capcom. It'll be very interesting to see where Platinum heads next.
Level-5 (Inazuma & Layton series grouped)
Professor Layton Series, DS & 3DS (2007-2011)
Inazuma Eleven Series, Wii, DS & 3DS (2008-2011)
Dragon Quest IX: Sentinels of the Starry Skies, DS (2009) *with Square Enix
Ni no Kuni, DS (2010) *with Studio Ghibli
Little Battlers eXperience, 3DS & PSP (2011)
Ni no Kuni: Wrath of the White Witch, PS3 (2011)
Girls RPG: Cinderelife, 3DS (March 2012)
Guild01 (Liberation Maiden, Aero Porter, Crimson Shroud), 3DS (May 2012) *with Grasshopper, Vivarium & Nex Entertainment
Time Travelers, 3DS, PSP & PSV (July 2012)
Professor Layton vs. Ace Attorney, 3DS (November 2012) *with Capcom
Inazuma Eleven GO 2: Chrono Stone, 3DS (December 2012)
Fantasy Life, 3DS (December 2012) *with Brownie Brown & h.a.n.d.
Professor Layton and the Azran Legacies, 3DS (TBA 2013)
Guild02, 3DS (TBA 2013) *with various
[B}Youkai Watch, 3DS (TBA 2013)[/B]
???
Whatever your thoughts on Level-5, they've undoubtedly established a very impressive range of franchises in such a relatively quick timeframe, but in the last year alone (presumably cautious of series fatigue) they have released (or are soon to release) five brand new IPs (counting Guild as one). Six 3DS titles released in 2012, only 3 announced so far for 2013, there's a good chance we will get one or two announcements for release late 2013 (Ni no Kuni 2 for 3DS seems pretty likely, maybe Inazuma 4), but as for the West, maybe a localisation or two will be announced at E3 (PLvAA, Guild02?).
Denyu-sha
Various Pokemon Mini titles (2001-2002) *published by The Pokemon Company
[...]
Math Play, DS (2006) *with Natsume
Demae Catering Channel, Wii Channel (2009)
Game Notes, 3DSWare (2011)
SwapNote/Nintendo Letter Box, 3DSWare (December 2011) *with Nintendo Network Business Department (NBD)
???
I thought I'd list these guys here just in case, especially since they could be due for a new release in the next year. Admittedly their software is small in scale but are generally of a first-party hardware app nature; they could be working on a SwapNote for Wii U, or something to do with the Near-Field Communication (NFC) functionality on Wii U.
Pokémon developers: Game Freak, Genius Sonority, Ambrella, Creatures Inc., & other The Pokémon Company developers
Pokémon Snap, N64 (1999, VC 2009) *HAL Laboratory & Pax Softnica
Pokémon Stadium 1-3, N64 & GCN (1998-2000) *HAL Laboratory, Creatures Inc. & EAD
[...]
Personal Trainer: Walking, DS (2008) *with NSD & Engines
PokéPark Wii: Pikachu's Adventure, Wii (2009) *Creatures Inc.
Pokémon Rumble, WiiWare (2009) *Ambrella
Pokémon Ranger: Guardian Signs, DS (2010) *Creatures Inc.
Pokémon Black and White, DS (2010) *Game Freak
Pokémon Rumble Blast, 3DS (2011) *Ambrella
PokéPark 2: Wonders Beyond, Wii (2011) *Creatures Inc.
Learn with Pokémon: Typing Adventure (2011) *Genius Sonority
The Denpa Men: They Came By Wave, 3DS eShop (February 2012) *Genius Sonority
Pokémon Black 2 and White 2, DS (June 2012) *Game Freak
Pokédex 3D Pro, 3DS eShop (June 2012) *Creatures Inc.
Pokémon Dream Radar, 3DS eShop (June 2012) *Creatures Inc.
Rhythm Hunter: HarmoKnight, 3DS (September 2012) *Game Freak
Pokémon Mystery Dungeon: Magnagate and the Infinite Labyrinth, 3DS (November 2012) *Spike Chunsoft
The Denpa Men 2, 3DS eShop (TBA 2013) *Genius Sonority
???
It's nearly time for Generation VI. Game Freak has historically taken 3-4 years between each new generation title, but even if it's pushed into 2014, we will surely see extensive previews and trailers some time in 2013. Recent comments suggest it may be a significant evolution of the game world. Meanwhile, Creatures has something out every year, maybe for Wii U this time (Park? Snap? Stadium?). Ambrella may be due for a new title too (Dash? Ranch? Rumble?) but hopefully they've improved a bit.