I judge them based on how much fun I had. A good story that makes me laugh can beat out bad controls, but gameplay that's unique and entertaining can trump a piss-poor story.
If I can play a game and say, I had a good time with this, then I judge it as a good game. If I play it more than once, or have fond memories of playing it, I consider it one of the best. Of my Top 3 games, the 2nd and 3rd placers, RE4 and FO3, are in there because I love playing them so much that I've beaten them so many times and logged so many hours in on them. My number 1, Sly Cooper 2, is number one because I think of the game so fondly that it makes me look at all the games I've played, and puts them to shame almost. It was just how fun I had playing that made it so good