Not my current list of favs but my favs if we count all the games in their libraries from a given time (this lis is BIG publishers):
1. Square-Soft (FF6, FF8, FF7, FF9, FF10, FF4, KH1, Chrono Trigger, Xenogears, Secret Of Mana)
2. Konami (Metal Gear 1,2, MGS1,2,3,4, Peace Walker, ZOE, Castlevania)
3. Nintendo (Super Mario World, DKC1,2, DKCR, MArio Galaxy, Maro 64, Zelda OOT, Zelda Wind Waker, Zelda Spirit Tracks, Smash Bros Melee, Brain Training, Metroid....)
4. Square-Enix (FF13, FF12, KH2, KH:BBS, TWEWY, Dissidia, FF7:CC, Dissidia, DQIX, Chaos Rings, Just Cause 2)
5. Capcom (RE1,2,3,4, Ace Attorney Series, Ghost Trick, Breath Of Fire, DMC)
Honorobale Mentions (SCE, Ubisoft)
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Top 4 independant devs devs:
1. Funcom (The Longest Journey, Dreamfall : The Longest Journey)
2. Rockstar (GTA3, San Andreas, Bully, LA NOIRE, RDR)
3. Atlus (PErsona 3,4, Shim Megami Tensei Devil Survivor)
4. Bioware (their independant days) ... KOTOR 1,2, ME1, Jade Empire
All hail the KING, Andrespetmonkey