While Wing Commander is my absolute favorite series, the third isn't the best of them.
TIE Fighter on the other hand is my favorite of the series, but I don't quite love X/TIE like WC.
There were great beat'em ups: Darkstalkers: The Night Warriors started the series and another personal favorite One Must Fall 2097.
Also notable from the year is the first Elder Scrolls game ES:Arena as beginning of a giant series.
But I really have only two options: FF6 and Live A Live.
FF6 is my favorite of the ones I've played (8 first). It certainly is the most iconic of all these.
And I hate to throw my vote to an obscure Other that'll likely get no second vote.
But my sincere opinion is that Live A Live is the best JRPG ever (with possible exception of Phantasy Star 1, but that's personal nostalgia), I have to vote that. Modern consoles are getting versions for a reason.