IMO, you can't make a top 100 list without either A Link to the Past or Ocarina of Time. You could easily make an argument for both titles being deserving of a top 20 spot. (A Link to the Past is my personal favourite). Super Mario World is also deserving, although they put Mario 64 there, so I understand why they left it out. The same goes for FFVI vs FFVII. I am missing Secret of Mana though, but then again they did put Chrono Trigger in, so..
As others have mentioned, at least one of LucasArts point&click adventures should be in it. Either Secret of Monkey Island or Indiana Jones and the Fate of Atlantis. Broken Sword is another classic adventure.
And I'd def put Silent Hill 2 before Silent Hill. Best horror game ever made, by far.