Best? I can't say Best because there are so many titles that are worthy to be up there with the best of em.
Kamui pointed out a couple of good ones...
Grandia 2 is responsible for making me miss my Calculus 2 midterm...(don't worry Grandia, I still love you). I played that game for 3 days around 12 hours each day. I just couldn't put it down... it was like "I'll just get to the next plot point and save..." 3 days later I beat the game and said to myself "Crap, I had a midterm this morning".
FF 6(3e) is my favorite RPG of all time because it's the first RPG I ever played... and what can I say, it was simply awesome.
The Wild Arms series is also another good one... WA 1 was great with its mixing of puzzles and good graphics(at the time... and a good musical score). For all the folks that hasn't played Wild Arms 1 yet it's getting released on the PS2 under the Title Wild Arms: Alter Code F(I believe). It's getting much better graphics and even more playable characters! Pick it up when it comes out.
Vagrant Story was a bit tedious at times but the way the characters interacted with each other... not to mention one of the best quotes from any videogame
"Shouldn't we wait for reinforcements?"
"Reinforcements? I
am the reinforcements..."
Bad-ass.
Star Ocean 2 for the PSX was a great game too... what other game lets you steal from your own party members when you're all taking a break(not to mention the 70+ endings)
Xenogears had a complex and intriging storyline which I thought was very well written... most people didn't like the 2nd disk but I thought it helped carry along the storyline faster and ultimately made the game better.
Xenosaga is also shaping up to be quite the series... I can't wait for the 2nd episode.
and last but not least
War of Genesis 3, and 3 part 2.
The storyline for these two games were simply amazing. Revelation after revelation in a manner that left me saying "holy crap..." when I finished the game... with a glimmer of tear as well(coming from me, that means alot).
You guys probably never played the game because it's not in english... it's a Korean PC game- I'm pretty sure you might've seen some of the artwork for it like this one
well I better stop my ranting... too many games to list