Atlus is probably my favorite of them all, I've never seen a game that they've made that I would consider anything short of good, they're kind to their customers, and they have a great backlog of games (such as Persona 4, which is one of my all time favorite games).
Monolith Software is also up there for me, they're games are always expansive and innovative, while at the same time the respect the player's time as well as the money they've invested into the product, and the games themselves tend to write their own conventions rather than feed off of cliche.
Capcom (as a developer, not a publisher) is also one of my favorites, having games like Monster Hunter, Ace Attorney, Resident Evil, and Dragon's Dogma (to name a few) also have a host of incredible games behind them, but the problem is...well, they're Capcom, and as a publisher they can get excessively greedy at times (though still not as bad as Activision and EA).
Square Enix is reclaiming its place for me. They too can be greedy, but in recent years they've been trying to innovate...everything. Games like Final Fantasy XIII, My Life as a King (and as a Darklord), The Last Remnant, and The World Ends With You are just some of the games that have shown that they have been listening to fans and critics and are trying to change up their formulas to keep things new and fresh (even if it's those same critics and fans that are bawwing because they are).
Though those are just off of the top of my head, though Atlus and Monolith are definitely two of my favorites (in that order), the latter two are simply notables.
Edit: Looking at Algo's post reminded me of another one that I can't believe I didn't add.
Level-5 is an incredibly talented, incredibly versatile, and incredibly innovative company that has so many conventional games behind it's back it's scary. Inazuma Eleven, which I discovered for the DS ("discovered", because it's not available in the States) is a jaw-droppingly fun Sports RPG that takes innovation in Sports gaming to new levels (it's rare for me to even look at a Sports title more than once); with it's deceptively child-oriented appearance, Inazuma Eleven is a game that actually has quite the dark story, especially for the message it tries to convey. On top of that, it's gameplay is deep and very fun, I'd say it (or rather, its sequel) is one of the best DS games out there and is certainly the best Sports Game in existence. That's just a single game. Then there's the various Dragon Quest titles that they've taken on, the classic Dark Cloud series, the ever-popular Professor Layton series, and a boatload of other titles and upcoming titles, Level-5 has truly given itself its place in Video Gaming History.
