Hmmm, why did I think there would be interesting discussion about the list. Should have realized it would be "IGN svcks" "those aren't RPGs" and "why isn't _____ higher/lower". Ah, well.
Personally, I'm just looking through the list to see how many I've played. It's running a bit under half, since there are certain platforms or series that I've just not dealt with (like, I never really played any Might & Magic, Ogre Battle, or Dragon Warrior. Did play Dragon Quest 8. Never did any Sega, or Nintendo besides SNES. Etc, etc, etc.)
So far it looks like:
90-100 5 or 6
Lunar ?, Shadow Hearts, FF8, Legend of Dragoon, Vagrant Story, Diablo 3
80-89 4
FO:NV, FF9, Shadowrun, Kingdom Hearts
70-79 4
Illusion of Gaia, Front Mission 3, Grandia II, Bard's Tale
60-69 4
Persona 3, Kingdom Hearts 2, FF10, Chrono Cross
50-59 4
ME2, Ultima 7, WIld Arms, Golden Sun
40-49 3 or 4
Xenogears, Pool of Radiance, Lunar:SSS, Suikoden II ?
30-39 4.5
Jade Empire, NWN, Morrowind, Fallout, (never played Poke Black/White, did mess around with earlier ones)
Kind of a mixed bag. With some of the older JRPGs, I played enough of them Way Back In The Day? that it's hard to remember exactly. (Like, I know I played a Breath of Fire, and I think 2 or 3 Grandia's, and a Suikoden. But not sure exactly which ones.

)
Yeah, it's a bit of an odd list overall. But it's hard for any "top 100" list not to be. Especially when it's on a wide-ranging topic.