Hmm. Tough call. I've played 1000's of games new and old. Its hard to call one best but.. I'm gunna have to go with:
X-Com: UFO Enemy Unknown
A friend of mine at high school in the time gave me a copy of this and it resulted in grades dropping, lack of social life, etc. It was the first video game where I found out the easy way that gaming can and will become an addiction.
It really was'nt for some kinda tight knit story that was scripted other than heres the aliens, they are expanding and you gotta stop them. The strategy elements though were some of the best approached still even today because you really had to wiegh out so many options in both fields of the game.
For example:
Asia is being attacked and my relations are already poor but I desperatly need the funding. My squad isnt that equipped and I'm in the dead middle of researching my next weapon set which I will have to manufacture, but.. I have no choice. I send my troops with poor weaponry against Discs of doom and crysallids only to have them mind controlled, paniced and running around killing each other. My relations with Asia drop anyway due to incompetance.
I'm in the field with my elite squad and I noticed an alien run in a building. I have found a few hostages and secured them, but there is still threats... but have I rescued all the hostages REALLY? I have the option of destroying the whole building or taking a couple troops in there and possibly have them killed due to ambush. Hmm.... I'll take my chances. I set the timer, throw it in a window and wait. The building turns to ashes. I see an alien corpse and hear the death screams of 2 civilians. Mission over, rating lost.
With an exception of something like Civ4, theres not many games that make me think that hard anymore. Scripted stories and stuff only go so far with me. Even todays Final Fantasy games feel way too much 'on rails' with me. Let me decide what goes on and this game was one of the few that actually allowed me to do that but still had a uniform progression and kept the two together quite well.