(In no particular order) My favorites are below:
*Ensemble Studios - The game Age of Empires (the first one) was what really sparked my interest in gaming. I played some SNES games, but was never really into gaming until I played AoE, then my love for Ensemble was permanent. A shame that they closed down, really is. All their games, excluding Age of Empires 3 (which still was very well done in my opinion, just not as good as their previous work), were phenomenal. They really left a mark on RTS gaming.
*New World Computing - One series that always come to mind when I think of a good strategy game is Heroes of Might and Magic. The third was my all time favorite, and to this day I still play the game. Again, a shame they no longer exist, and I hate what Ubisoft is doing to the title.
*Blizzard - Another icon in RTS gaming is Blizzard. With Warcraft: Orcs and Humans and the series it spawned, I love the lore, and the gameplay of all their RTS games. Starcraft really set the standard and is recognized as one of the best, if the best RTS title. The balance between the 3 races was near perfect, and their is still a large competitive community playing the game. Other games such as Diablo left some good memories of me and friends staying up all night playing.
*Bioware - Knights of the Old Republic... Mass Effect... Dragon Age... Nuff' said. One of the best RPG developers. Their lore in their games is (to me) even better than the lore in TES (but not by much). I can really sit there for 30 minutes listening and reading codex entries in Mass Effect, and truly get immersed in the universe. Dragon Age lore wasn't as impressive, not that there was lack of it, simply that it is sort of generic. But the gameplay by itself is truly great, and the squad gameplay is as fun as anything.
*Valve - Where to begin? They have so many types of games it is hard to focus on one... well actually I take that back. Half Life. The first shooter I really liked, and the story is great also. (Where are you Episode Three!?!) However, they have many other great games! Team Fortress and Left 4 Dead are both great teamwork games, and both have a great online community that is still running. Their first-person puzzle game Portal is unmatched! One of the best, Valve is.