Yeah, I don't disagree on the Top 5, but there are some comments to make on this list.

-Final Fantasy IX is too low. No way The Legend of Dragoon should be above it.
-Fire Emblem on the list is . . . interesting. As much as I love the series, I don't really consider it to be a true RPG. Then again, it and other SRPGs share other core tenets with other RPGs, so I'm not opposed to it.
-Demon's Souls being on the list is great. It would have been a huge oversight if it weren't.
-Final Fantasy Tactics Advance is a personal favorite of mine, but I think it's a little too high in the list.
-Thankfully, Skies of Arcadia is on the list. If it weren't, I'd boycott IGN's gaming section forever.
-Freedom Force is the first game on the list that I can say that I never heard of before reading about it there. Then again, knowing Ken Levine and Irrational, the minds behind System Shock 2 and BioShock, it's hardly a surprise.
-Tactics Ogre is a series I've been interested in, but the fact that I was never much of a Sony system owner prevented me from getting into it. Too bad the Vita is a freaking joke, and I have no interest in the PSP.
-I approve of Dragon Quest V on the list. I haven't played it myself, but I've watched an entire LP of it. I can tell just from watching that it's one of the greats.
-As much of a Pokémaniac that I am, I don't think Black and White should be quite so high.
-I was fully expecting fanboy outrage over VII not even being in the top 10. I'm pleasantly surprised.
-Where is Deux Ex: Human Revolution? I know it's not going to be in the pantheon, but surely it's somewhere in the top 100?
-Oblivion should not be above Morrowind. As much as Oblivion was an improvement in gameplay overall, it regressed when it came to atmosphere, mood, and all of those other little details that make a game immortal.
-I might get flak for this one, but Dark Souls fully deserves this placement. It's one of the best games to come out in this console generation, and it's one of the best to come out in recent memory.

If nothing else, this list is a nice compilation of games that I need to play sometime in the future.