My favourite is VI, why? Memorable, loveable characters. Locke, Celes and Edgar were especially good. Don't even get me started on Kefka. One of the better plots in the series, fun gameplay that rarely required grinding and an awesome soundtrack to boot. Tactics is a close second for the mature plot, epic atmosphere(I'm a sucker for atmosphere) and good job system.
On a list of best to worst...
VI
Tactics
X/IX
^
V
IV(DS ver.)
TA/TA2
Crisis Core
IV
XII
VII
Revenant Wings
VIII
Crystal Chronicals
I
III
XIII
II
X-2
Mystic Quest
A raw turd
Dirge of Cerberus
I'm probably forgetting something.
On a list of best to worst...
VI
Tactics
X/IX
^
V
IV(DS ver.)
TA/TA2
Crisis Core
IV
XII
VII
Revenant Wings
VIII
Crystal Chronicals
I
III
XIII
II
X-2
Mystic Quest
A raw turd
Dirge of Cerberus
I'm probably forgetting something.