The Legend of Zelda - You can SAVE your game and come back to it, never been anything like that before
Super Mario 64 - 3D platformers and graphics changed forever, not my favorite N64 game but I respect what it did for the industry
Doom - Perfected what Wolfenstein did and led to the most successful genre in video games
Skyrim - I really think it is a game people will look back on as having a huge impact on the industry. This type of game was supposed to do well and have a niche audience, that is far from the case and was a massive success that says "You can make a nerdy ass game and people will buy it, you don't need to make a game to the lowest common denominator to sell."
I think this is a pretty good list. I wouldn't have thought about Skyrim at first, but it's impact is definitely being felt in terms of the open world genre.