I couldn't think of any, and then I thought of eight :D

I loved every perfect moment of:

Planescape Torment
No One Lives Forever
Deus Ex
Bioshock (hey, this is my list ;)
The Secret of Monkey Island
Grim Fandango
Dungeon Keeper
Legend of Zelda: Ocarina of Time

That isn't just a list of favourites; I have a couple of other titles (particularly with the two adventures there) that I'd put just a little ahead of some of those, but they have at least some aspect I'd change if possible to do so. However with these, I reckon the sum of their whole is perfect and not to be tinkered with at all. Even their graphics each has a style that works just as it is and that a remake wouldn't improve upon (TSoMI special edition, case in point!).

If I may totally degrade and derail this thread by quoting the late great George Carlin, "I never fucked a ten, but one night I fucked five twos."

Homeworld is damn near perfect in my eyes. All it really needs is a mod for current gen graphics and its good to go. That would make it about as close to perfect as you can get.

I think Phoenix Wright: Ace Attorney is pretty close, for what it sets out to do. But I can imagine anyone playing it and not liking it as well.

Well, according to your definition, a perfect game would be one where I wouldn't change anything.

Yes, it is called Majesty.

Why, simple, it combines the best elements of the games I like: RPG, God-like and a bit of strategy.

RPG because your units gain experience as long as they survive the battle.
God-like because your units have a will on their own which you can't control directly.
Strategy because you have to think how you are going to develop yourself (since building certain buildings blocks you from building others).

So, I wouldn't change anything in that game.

Still, I consider the best game to be Darklands.

Never played a perfect game.
Closest was probably Ultima Underworld.

Deus Ex
Doom II
The Scarab of Ra
Trinity (text game)
Jagged Alliance 2
Civ IV Beyond the Sword
Torchlight

But, perfection (as in, wouldn't change anything) isn't the most interesting to me. I like scope, ambition, sprawling gaps between sublime moments of transcendence and deadend moments of failure. Games like that for me are:

Arcanum
Vampire The Masquerade Bloodlines
Fallout: New Vegas
Fallout
Fallout 2

Agree mass effect 3, what made it the most memorable for me is that i already saw the shitty ending, therefore every moment leaving up to the shitty ending was well memorable

I think I have to go with Breath of Fire 3.
I just happen to like everything about that game.

Chrono Trigger also came pretty close, except for the lack of a really tough opponent for a newgame+.

The perfect game? Doesn't exist =/

But I really enjoyed these so much that I'd almost call them perfect:
-Amnesia: The Dark Descent
-Castlevania: Symphony of the Night, Harmony of Dissonance, and Aria of Sorrow
-Dynamite Headdy
-Final Fantasy 5 and 6
-Legend of Zelda: Ocarina of Time as well as Link to the Past
-Mirror's Edge
-Paper Mario as well as The Thousand-Year Door
-Prince of Persia: The Sands of Time
-Shining Force 1
-Sonic 1-3
-Soulcalibur II
-Super Mario Galaxy 1
-Super Meat Boy
-Super Metroid
-Super Smash Bros Melee
-System Shock 2
-Xenoblade Chronicles

There's much more (trying to remember and figuring out the name)...but it would take up a lot more space.

Grand Theft Auto 3 was pretty perfect when it came out for me. I was just in awe of it and had zero complaints, as far as I can remember. Today it's pretty clunky though, obviously.

Can't remember anything else that felt flawless... My two favorite games, Morrowind and Deus Ex, had annoyances even in their release period.

I'll have to go with Planescape: Torment. I remember when I first brought it home and wanted to try it out. I played for some time without checking what hour it is... And suddenly I realized it's 5 AM and I have to go to school in two hours.
If I may choose another near-perfect game, it'd be Grim Fandango. I don't know why, but somehow it made me care for those characters and wish them best. Graphics, puzzle\story integration, memorable characters... comes very close to perfect.
Sanitarium would have a chance to appear here if the devs cared enough to keep the mood from first four chapters and introduce something better than cyclops, bugs and Aztecs.
Those three games I replay every year and still enjoy them.
All signs point that another game that is, in my opinion, near perfect comes to GOG today : )

The first game I thought of was Metal Gear Solid, but that's not quite perfect because it could use more sophisticated graphics and gameplay. Now, of course, that's precisely what Twin Snakes is, but that's not perfect because it wasn't designed to have first person, so it kind of deforms parts of the game. Also, MGS 2 has improved graphics and first person and lockers, but it's not perfect because what the heck, vampires? (Yeah, yeah, nano-machines.) Other than that, it approaches perfection.

The second game I thought of was Zero Escape: Virtue's Last Reward. But, while I love this game to death, it is a bit rough around the edges. The 3D character designs are not as beautiful as the sprites of the previous game, the translation, though brilliant, has several embarrassing typos, and, yeah, there's a potentially save-erasing glitch. Bleh.

But when I thought about this: I decided there was one game that I would change nothing about: Ghost Trick: Phantom Detective. While it might not be quite my favorite game of all time (though it's at least very close), what it does, it does perfectly. The story is brilliant with some insanely good twists. The graphics are stunning. The gameplay is original, clever, and well implemented. It's as good as it can be.

Two I can think of: Fallout 2 & Gabeirl Knight 1

Abe's Exoddus.

While objectively it has it's flaws, there is nothing about it I would change.