I have a few different "best game" categories.
The "if you were stranded with only one game" scenario. It would have to be a long game WITH good replay value as well as good. I'd go with Chrono Cross. Many different endings, many different characters to collect. Great gameplay, great music, good story. In that best game category... Chrono Cross.
The "most time played" category. I mean if I've spent more time playing it than any other game, it must be the best and my favorite, right? That would be n64's Perfect Dark. Mainly because the multiplayer vs bots and co-op mode was a daily activity for me and a few friends for years. My savegame racked up nearly 300000 kills. I still consider it the best shooter of all time.
The "because everyone else says so and It's just really that good" category. Many to chose from, Shadow of the Colossus, Zelda OoT, Fallout 2, that kind of crowd. But I'd have to say Silent Hill 2. Love survival horror, and it's the high end of survival horror. With Eternal Darkness right behind (because not just horror, but Lovecraft horror.)
The "most important" category. This one is surprisingly tough. Minecraft is a possibility because of all of the random generated goodness. Of course Doom showed the masses what first person shooters could be. Hell, the "nemesis" system in Shadow of Mordor is something that I think GREAT game franchises could be based around. In that sort of setting, as well as doing something similar with (example) an open world prohabition-era gangsters game, A "Game of Thrones" style high fantasy with rival houses, the list is endless. However in the end "most important" almost went to Zelda OoT. It DID show us that a franchise could not only improve but become so much more while staying VERY true to the original game when stepping up a console and changing it's format some. But in the end I'd have to say Ultima VII. Because it did that same thing (the earliest ultimas were basically little more than text adventures) but it was an early example of SEVERAL game conventions that have become commonplace today. Open world, party system, inventory system, real time, hunger and thirst, persistant changes to enviornment, reaction to criminal behavior (hell lots of NPC behavior...) and probably a lot more I'm forgetting. Ultima VII may have been one of the most important games ever made. Oh and the Hoe of Destruction.... priceless.
There's probably a lot more "best ever categories," but this post has gone on too long as it is.