+1 on Abe's Oddysee. It's well over ten years and it still holds up very strong in atmosphere, level design, story and even cutscènes.
Unreal 1. It's like every singleplayer shooter after that was a step down. Except, of course...
Half life 2. I only played it years after launch, but the praise it got at release was just...worth it absolutely.
Donkey kong (Game boy). Lots of levels, decent difficulty, funny, decent music...
Rollercoaster tycoon. Perhaps I should say "RCT 2 with all the expansions", but adding more tools won't make it more perfect than it already was.
Starcraft 2. Best RTS ever. It took years for blizzard to make it and even more to tweak it, but there's no getting around it: there is a flaw downright NOWHERE.
Sort of undecided on:
999. The story is hands down magnificent and the way it is told is awesome. It's just that I barely have any experience with these kinds of games to judge it by.
UT2004: it's my favorite game of all time, but I can't get around the fact that the movement system was so quirky that online matches were...pretty weird to watch, really.
Rayman origins. Yes, it's the best platformer on the wii (save perhaps newer super mario brothers wii) and I can't point anything flawed on it, but still...I'd say it's great, but not perfect.
Race the sun. It certainly has everything going for it: endless landscapes, fitting music, simplistic but decent graphics, a little bit of RPG...there is nothing to add or take away, but still...perhaps it's just the small scale of the game, but it's just "great"
Braid. this one is certainly worthy of being perfect, but the puzzles weren't always my cup of tea. And I sometimes felt more like doing trial-and-error than actually puzzle solving (could be me...I suck at this).