The top 100 list thingy that I planned to start will come eventually, but unsurprisingly, most of the games on here are on there.
If I were to make up the list from scratch, well, hmm. I can see you're trying to keep it balanced across era and genre, so it's tough to add. Some kind of strategy/puzzle game should be included, though, so I would think Civilization should be an automatic. The only WRPG on there is World of Warcraft, so something non-MMO should have made the list as well, whether that's Elder Scrolls, Fallout, Baldur's Gate, or whatever else. (Or is that what GTA3 is?) Also a "shooter" (and I don't mean FPS) might have been nice, unless you're counting Space Invaders in there, or arguably Contra.
I'd probably have left the Duke off there; he's noteworthy, but not top-50-worthy. I was never really aware of the existence of KoF until it was basically done, either. However, overall it's a really good list.
If I had to add 10:
51. Civilzation IV
52. Pac-Man
53. TMNT 4: Turtles in Time (would do original arcade, but you have that era saturated)
54. KOTOR
55. THPS 2 or SSX Tricky
56. *some* non-racing sports game...Madden is most obvious choice
57. some highly casual game besides The Sims. Minesweeper would be my pick.
58. Star Fox 64
59. Asteroids
60. Morrowind
And that's just to stick to your spread-it-around philosophy. There's a ton of other games that I think are deserving, although I admit a list of 50 is rather restrictive. If I made such a list, it would probably be inundated with old games, like Asteroids, Joust, Combat, etc.