KQ6 is a given for me; the atmosphere, the soundtrack (which I blasted on my iPod and shamelessly whistled along to while walking to town the other day), the characters, the story... Everything is perfect about it.
I like KQ7 (again, great soundtrack), since it got me back into the series after it was long lost in my mind as a little kid. It was one of two pieces of software (the other was an interactive encyclopaedia) that came with our first PC.
Despite never having completed it before (I've shamefully only completed three of the KQ games, but watched the rest on YouTube and loved them!), I have recently totally fallen in love with KQ3, if only for the opening scene. The music just sets the atmosphere perfectly and the story is really gripping. I can only imagine the controversy Gwydion caused when he was the protagonist instead of Graham (who confusingly stayed rather yellow for this game!).