This is a tough question to answer, for me anyways. I make distinctions on "best I've played" versus "my personal favourites", and among those categories I also see several classes based on several other factors.
So, to answer the thread literally, the best games I've ever played include (in no order):
Morrowind
C&C: Red Alert
Thief II
Final Fantasy 9
I consider these "best" in terms of technical quality, atmosphere, story, sounds, music and gameplay value. They excell in all categories (in context of the years in which they were each released). They're not only well-made, but fun and full of gameplay and variety.
My favourite games, on the other hand, are:
Legacy of Kain (series)
Final Fantasy 7
Creatures (series)
I'm particularly fond of LoK's sprawling, mind-fuckingly complicated storyline, and deep, interesting characters.
FF7's characters, story and atmosphere are immersive and addicting; this was the first FF game I ever played, so nostalgia plays a big part in this choice. However, I'm not going to appease the Internet's currently fasionable group opinion by pretending this isn't my favourite game in the world, or say that it's "sooo overrated", despite having heard that phrase spoken in this context about five million times in the past few years by all the kids who want to stay kewl and up-to-date with current popular trends. Something isn't "overrated" because too many people like it, and it's not edgy to deliberately have the opposite opinion for no other reason. Damnit. </soapbox>
As for the Creatures games, I'm chalking that up to nostalgia, plus my love for toying with AI and watching procedural/unpredictable behaviours, and no other application or game has ever come close to the realistic nature and complexity of these endearing little animals. <3