Konami. They make the Suikoden series, and tons of other great games across many genres, and have for many years.
I also like Square-Enix, even though I'm not a huge Final Fantasy fan, for lots of other RPGs they make, like Seiken Densetsu 3 (prequil to Secret of Mana, iirc), which I just recently played through, and Chrono Trigger.
Koei is also awesome, they make the Dynasty and Samurai Warriors games, along with Nobunaga's Ambition, Kessen, and other more tactical games. I've always loved beat 'em ups, and Koei's one of the few companies still making a bunch of them, and while they do some creative retelling to make the story not always exactly the same, they still do an admirable job of incorporating history into their games along with (sometimes) an "Encyclopedia" feature to look up what actually happened. Th games helped me learn about the Sengoku and 3 Kingdoms eras and lead me to reading more on those periods.
I haven't played many Sony-made games, but all the ones I have played (such as Legend of Dragoon and Genji: Dawn of the Samurai) have been excellent gems.
I already named plenty, but seriously...no one (or no one else) for Konami, Nintendo, or Sega?!