Not a bad list, though I feel Chrono Trigger should get top spot for what it does as a game and as a narrative. Not that I don't love VI it's just CT is easily my favorite game of all time.

Other than that...

Praise:
Lufia 2, Lunar 1 and 2, Wild ARMS, Suikoden II, FFIX and BoFIII
Top 25 was mostly good
Like Laddy, I feel it's a good mix of WRPG and JRPGs
FFTactics Advance and Ogre Battle March of the Black Queen got on the list, and were ranked decently.
Got most of my top favorite games on there.

Scold:
Some of the rankings are off, P3, P4, and Vagrant Story should both be much higher on the list, FFIV and Wild ARMS should probably be lower despite my love for both of them.
Snubbed Valkyrie Profile (despite not liking the game, it deserves a mention) Shin Megami Tensei III, KH: Birth By Sleep, BoFIV, and Suikoden III and V. Not to mention FFV.
I honestly don't feel KH2 belongs on this list, same with FFVIII
I will echo Bolivar and say I am not too keen on the idea of MMOs being on this list, but sadly I can't come up with a good enough reason to disqualify them without it also pertaining to a third of the list.