Nintendo, Platinum Games, and Bioware. Although, Bioware has been slipping for me lately.

Favourite publisher: Take-Two interactive ( GTA, Red dead redeption, Borderlands, Bioshock, NBA 2k, XCOM, Civilization, Midnight Club, Max Payne 3)
Favourite studio: Bethesda Game Studios (Elder Scrolls and Fallout)

tho Nintendo is very high up there too (for publisher and developer)

honorable Mentions:
Bizarre Creations ( Project Gotham Racing, Blur, Geometry Wars)
Criterion Games (Burnout series, Need for Speed Hot Pursuit and Most Wanted 2012)

Nintendo
Blizzard
Capcom
Platinum 
Naughty Dog

Bioware is disappointing. They are in detention. 

1-Nintendo 

2-Kojima Productions 

3-Atlus

4-CyberConnect2

5-Naughty Dog

Well, as for the publishers that make my favourite games, it'd be Nintendo, Capcom and Square Enix.

XSEED games/Marvelous Entertainment are probably my favorite publisher, because when they localize a game they localize it RIGHT. They also pick up games that most wouldn't, are very welcoming towards fan feedback, and come on... They've published YS, The Last Story, Pandora's Tower, Ju-On, Fragile Dreams, etc. Awesome games that were probably not making their way to the west without them or Rising Star Games.

Bandai Namco, Nintendo, SEGA, and Square Enix have all published many of my favorite games. And so has Capcom! But the latter has done some incredibly off putting things.

Developers wise.... If Tri-Crescendo are still active, then they're my favourites. The few games I've played from them have left a huge impact in me. Baten Kaitos, Eternal Sonata, and FRAGILE DREAMS are all works of art that have a very, very special charm that you'd be hard pressed to find somewhere else.

Again, Nintendo/Bandai Namco/Capcom/Square Enix have all developed some of my all time favorites, and I'll always hold them dearly for that.

Special mentions: Gamefreak, TOSE, Hall, whoever developed the Twisted Metal games, which wasn't Sony.

Publishers: Nintendo and Square-Enix
Developers: Nintendo EAD/EPD, Squaresoft/Square-Enix, Monolith Soft, Level-5.

Atlus and Nintendo

The only ones I feel I really like currently are ATLUS and Nintendo, as they've consistently released games I've really enjoyed over the years. There were others I liked, like CAPCOM and Square, but they're fallen from grace for me, and still haven't gotten back to those high standards I remember them being.

90s Square , Capcom , SEGA