If someone can do a list similar for Microsoft and Nintendo, I will add to the OP.
Attempting Nintendo:
Internal Software R&D
Nintendo Entertainment Analysis and Development (5 teams)
Nintendo EAD Tokyo (2 teams)
Nintendo Software Planning and Development (4 teams)
Nintendo Software Design and Development
Nintendo Network Service Development
Nintendo Software Technology Corp (2+ teams)
1st Party Studios
Intelligent Systems (3 teams)
HAL Laboratory (2+ teams)
Retro Studios (2 teams)
Monolith Soft (2 teams)
NdCube
Brownie Brown
Project Sora
Genius Sonority (minority stake)
3rd Party Partners (developed at least one 1st party title in the past 2 years or handles long running series)
Alphadream (Mario & Luigi series)
Ambrella (Pokemon spinoffs)
AQ Interactive (Flingsmash, The Last Story)
Arika (3D Classics line, Metal Torrent, Endless Ocean series)
Arzest (Wii Play Motion)
Asobism (FreakyForms)
Camelot Software Planning (Mario Golf/Tennis series, Golden Sun series)
Chunsoft (Pokémon Mystery Dungeon series, Wii Play Motion)
Creatures Inc. (Pokemon series and spinoffs)
Curve Studios (Fluidity)
D4 Enterprise (Snapdots)
Eighting (Master of Illusion series)
Game Freak (Pokemon series)
Ganbarion (Pandora's Tower)
Good Feel (Kirby's Epic Yarn, Looksley's Lineup, Wii Play Motion)
Grezzo (Line Attack Heroes, Ocarina of Time 3D, Four Swords AE)
Headstrong Games (Battalion Wars series, Art Academy)
indies-zero (Cooking Guide series, electroplankton series)
Jupiter (Picross series, Personal Trainer series)
Keynet (Thruspace series)
Koei (Pokemon X Nobunaga)
M2 (Fossil Fighters series)
Mindware (Flametail)
Mistwalker (The Last Story)
Mitchell Corp (Polarium series, Wii Play Motion)
Monster Games (Excite series, Pilotwings Resort)
MuuMuu (Saru Band)
Next Level Games (Mario Strikers series, Luigi's Mansion 2)
Paon (Aquaspace, Donkey Kong spinoffs)
ParityBit (Calciobit)
Poisoft (Sakura Samurai)
Prope (Wii Play Motion)
Q-Games (Trajectile, Starship Defense, X-Scape, Star Fox 64 3D)
Red Entertainment (Fossil Fighters series)
Sandlot (Zangeki no Reginliev)
Sega Sports Design R&D (Mario & Sonic Olympics series)
Shift (And Kensaku)
Skip (Art Style series, Chibirobo series, Snowpack Park, Wii Play Motion)
Square Enix Osaka (Mario Sports Mix)
SynSophia (Style Savvy series)
Team Ninja (Metroid Other M)
Tecmo (Spirit Camera)
Treasure (Sin & Punishment Star Successor)
Tose Software (Starfi series)
Vanpool (Tingle series, Wii Play Motion)
Vitei (Steel Diver)
edit: Since the OP included 3rd party owned IPs like PixelJunk and Quantic Dream's games, I decided to add a similar list for Nintendo.
3rd Party Publishing Partners
Activision (Goldeneye 007)
Big Fish Games (Mystery Case Files series)
Capcom (Ghost Trick, Monster Hunter Tri, SSF4 3D Edition, Resident Evil Mercenaries/Revelations)
Disney (Epic Mickey)
Hudson Soft (Tetris Party Deluxe, Rooms, Tetris Axis)
Level 5 (Professor Layton series, Inazuma Eleven series)
Namco Bandai (Solatorobo)
Omiya Soft (Culdcept 3DS)
Paon (Glory of Heracles)
Square Enix (Dragon Quest series, Fortune Street)
Tecmo Koei (Fatal Frame series, Samurai Warriors 3)
Ubisoft (Just Dance Wii)
Warner Bros. (Lego City Stories)