Never played a perfect game. Here are all my favorite games and why they aren't perfect games:
Final Fantasy Tactics - Has effectively no tutorial, making it very difficult for new players. Once experienced, the game is very easily broken. This is furthered by the ludicrously overpowered unique characters recruited in the last chapter of the game. In addition, the original version's translation is less than stellar, leading to some ambiguous developments in the plot (this is far and away fixed in the PSP version).
Chrono Cross - Had a good many completely useless characters. At times the plot was ludicrously convoluted. The solution to the final boss that beats you the game (the real way) is ridiculous and is generally not possible if you don't know what you're doing, or that you aren't suppose to kill the last boss.
Shadow of the Colossus - Has incredibly frustrating controls at times. The collision detection is quite off in areas leading to odd animation glitches. It's probably the closest to perfect of any of the games on the list.
Mass Effect 2 - Story and gameplay have a massive disconnect, as I see it. Gameplay is unvaried, as are solutions to problems the game presents.
Grim Fandango - While being a fun time due to its sense of humor and story, isn't all that well designed as a game. Suffers from the main problem of all adventure games of that era.
Castle Crashers - Isn't in any way complex or even varied.
That's basically my top 6... I don't think any of them are close to perfect.