Total Annihilation for me.

Star Control II: The Ur-Quan Masters.
(The avatar should've been a dead giveaway.)

For all the crap that game gets, i bought and finished the N64 version, twice. It was nothing great but it wasn't as bad as some people make it out to be.
My choice for best game goes to ROGUE, that little text only game from the eighties. It was one of the first games i ever played and it made me a gamer, it made me take an interest in games in general and RPGs in particular, some of the best selling games out there (Diablo series for example) are direct descendants.
Most of Rogue's features, such as endless replayability, randomly generated content, and so on are major selling points for games today. Also, it has been ported to almost everything under the sun, from the ancient Commodore 64 to the Nintendo DS.

It's hard picking my favorite of all time.
All I can say is that SMB3 is the one game that made me decide I was NEVER gonna give up playing videogames.

This is a very difficult question because most of us like different games for different reasons, picking one just isn't fair really.
But if I must then...
Quake! It was the first real 3d game I am aware of, had/has a brilliant community, immersive gameplay and great multiplayer. It took the world by storm for good reason.
Wouldn't be my favourite game though, but that's not what you asked.

Im surprised it came up, but my vote would be Dungeon Keeper aswell.

I don't think it's my favorite of all time or necessarily the best, but in a thread like this I think Shadow of the Colossus or ICO deserves a mention. If only for feeling fresh and different (IMO of course) when it came out.

So many great games so little room.
Ok to choose just ONE SINGLE game I have to go with.................
Master of Orion 1

Also, I think the graphics could use an update, don't you think?

Another problem is that you can't pause the game or fastforward.

At least you can take screenshots. And the play control is fantastic! (Unless your avatar is intoxicated on something. Then it gets kind of difficult.) Also, there really isn't any level grinding, unless you're playing a jock or a doctorate student!

I don't know... I get bad enough framerates as it is, I'd appreciate an option to turn down some of the effects.

I can turn down the effects on my monitor. All I have to do is have my avatar take his glasses off. The resolution drops SHARPLY and the depth of field loses reliability.

Doom.
If only becasue it spawned the greatest comic of all times.
RIP AND TEAR. RIP AND TEAR YOUR GUTS.
YOUR HUGE, YOU MUST HAVE HUGE GUTS.
RIP AND TEAR.
Plus the GREATEST SHORT STORY of ALL TIME:
DOOM: Repercussions of Evil
John Stalvern waited. The lights above him blinked and sparked out of the air. There were demons in the base. He didn't see them, but had expected them now for years. His warnings to Cernel Joson were not listenend to and now it was too late. Far too late for now, anyway.
John was a space marine for fourteen years. When he was young he watched the spaceships and he said to dad "I want to be on the ships daddy."
Dad said "No! You will BE KILL BY DEMONS"
There was a time when he believed him. Then as he got oldered he stopped. But now in the space station base of the UAC he knew there were demons.
"This is Joson" the radio crackered. "You must fight the demons!"
So John gotted his palsma rifle and blew up the wall.
"HE GOING TO KILL US" said the demons
"I will shoot at him" said the cyberdemon and he fired the rocket missiles. John plasmaed at him and tried to blew him up. But then the ceiling fell and they were trapped and not able to kill.
"No! I must kill the demons" he shouted
The radio said "No, John. You are the demons"
And then John was a zombie.

Why? It's the most realistic and up-to-date graphic simulation I've ever seen!