One thing that I hate is "best of" lists that confuse "best" with "no influential."
For example, 2 things on this list (counter strike and HL2) were, arguably, pretty decent games at the time and has so innovative elements to them. But, in the years after them, there have been many games that take their same formula and just do them better and I will argue that those later games are indeed better games, just not as influential.