I’ve already mentioned Xenogears, so I doubt this is much of a surprise. It’s practically the perfect RPG even with obvious flaws; if budget and time hadn’t caused certain parts to get left out (and if the translation was better) it would be my unquestioned favorite game in any genre.
The story is the best, most complex, and deepest of any video game ever made, with the most developed characters around. Religious and psychological symbolism that actually makes sense, romance, a search for identity, and more backstabbing than Final Fantasy Tactics. (Figuratively. FFT probably holds some kind of record for the amount of literal stabbing.)
The music is just amazing; one of the most emotional video game soundtracks ever.
The battle system is still fine, though the concept involved has been done better since.
Homages and references to anime and classic sci-fi all over the place (a few of the more obvious include Childhood’s End, Soylent Green, and Macross), but it’s still entirely it’s own thing.
The graphics….well, you can’t have everything, but they hold up better than FF7’s do at least.