Origin Systems Inc. (Post EA acquisition till 2000)
Archetype Interactive (Mid-Late 90's til Near Death Studios era)
Sony Online Entertainment (Late 90's Era - Verant Interactive)
NCsoft Corporation (Mainly late 90's, but still applies today)
Mythic Entertainment (1995-2006, After EA buyout it does not count)
Artifact Entertainment (Early 2000's and Late 2000's as Virtrium LLC)
Square Enix Company (Early 2000 as Square Company, Mid 2000's as SE)
Blizzard Entertainment (Condor, Blizzard North - Mainly, but rest still apply.)
ArenaNet Inc. (NC Seattle since NCsoft acquisition in 2002)

To me these are the only companies that have mattered to date. I can name plenty more, but it's not worth the effort at all.

With the 9 companies I mentioned above you have gotten Ultima Online, Meridian 59, Everquest, Lineage (series), Dark Age of Camelot, Horizons: Empire of Istaria, Final Fantasy XI, Diablo (series), World of Warcraft, and Guild Wars (series). These are the games that have honestly shaped the genre of MMOG's as we see them today.

I did not list FPS devs, but if you need them I'd say that Id Software, Valve Software, and Epic Games are really the only ones that have truly shaped the industry. Although, I do have a soft spot for Sierra and Gearbox as well.