In my opinion, the problem with lists like these is that games that were groundbreaking 20 years ago are relatively simplistic by today's standards. (In other words, Super Mario Bros. was an incredible plaformer at the time of its release - and it remains a good game to this day - but is it really "better" than the recently-released but much less influential New Super Mario Bros. Wii or Rayman Origins?) Accordingly, lists that try to determine the "best" games of all time usually end up blending the "best" games with the "most influential" games.
I have only seen two lists that ever nailed it. The first appeared in EGM's 100th issue:
http://kirkjerk.com/vgames/powerlist/egm100.htmland it is hard for me to argue that the games on this list were not the "best" games available in 1997. The second appeared in EGM's 200th issue:
http://www.1up.com/features/egm-200-greatest-videogamesThis list contains the best of games of
their time, and I read it as a list of the "most influential" games.
(It is important to note that, since EGM was a magazine about consoles, it excluded PC games from both lists. Accordingly, some classic PC games such as Doom, Starcraft, etc. do not appear on either list.)
EDIT: That said, I consider Super Mario Bros. to remain one of the best, most influential, and most perfectly constructed video games of all time. For me, it would rank very highly on both a list of "best" games and a list of "most influential" games.
