Many of you complain when two or three of your favorite games do not make it on the list...
As for Super Mario Bros. 3, I am not sure why they decided to not put it on the list. I guess many of them thought it was a big upgrade of the original Mario Bros. Super Mario World and Super Mario World 2 were both different from each other in their eyes and that can be justified.
Final Fantasy 7 is highly questionable. To include FFX, but not to include the game that popularized the series in America...very questionable.
And I am glad for once Final Fantasy II beat Final Fantasy III. Final Fantasy II was the game that introduced many RPG concepts such as classes. It was also the first to have memorable characters, and one of the first to have a plot. Final Fantasy III may have been great, but it did not really introduce new features or concepts to the RPG genre as a whole.
Remember, the criteria for this list is how revolutionary a game is, the game's influence in its respective genre and the game industry, and how fun it is back then and now.
On a side note, Tetris dominated in EGM, EW, and IGN's list. In EGM, it held the #2 rank, only behind Super Metroid. In EW, it held the #3 rank, behind Doom and Zelda. In IGN, it held the #4 rank. Glad to see all three publications put it in their top five.