Here's my top 20from my full list of ranked RPGs completed (with some comments added):
20 - Xenosaga Ep. I: Der Wille Zur Macht (PS2) -- because, unlike the rest of the gaming populace, I LIKE 40 minute cut scenes. Deal with it.
19 - Seiken Densetsu 3 (SNES) -- because it's awesome.
18 - Secret of Mana (SNES) -- also because it's awesome. Just, slightly more awesome, I think... on a personal level, I remember it more fondly.
17 - Final Fantasy VII (PS) -- You can beat up on silent protagonists (Cloud "..." Vincent "...") all you want. The materia system was hot, no lie.
16 - Alundra (PS) -- Surprisingly dark plot, cool character designs, decent localization from Working Designs, and one of the best soundtracks Kouhei Tanaka ever penned (I prefer it to any and all Sakura Taisen soundtracks!).
15 - Zelda II: The Adventure of Link (NES) -- the only true "RPG" among the Zelda games (remember leveling up?!), I could play this game over and over and over and not get tired of it.
14 - Super Mario RPG (SNES) -- Axem Rangers. Enough said.
13 - Final Fantasy X (PS2) -- Because it made me cry. A bit. And sphere grid is <3.
12 - Kingdom Hearts (PS2) -- The opening cut scene won me over. The rest was just details. So I'm a graphics whore now and then. Deal with it.
11 - Kingdom Hearts II (PS2) -- See the last one. And add in a Gummi Ship mini-game that didn't suck. There you go. (oh, those time-attack Triangle Button maneuvers were good too)
10 - Romancing SaGa (PS2) -- Among Square (Enix) games, you can't get much more "niche" than the SaGa series. I know that. But man...this remake was fan-freakin-tastic. This was the most SURPRISING experience I've had in RPG-dom for the last 5 years. I didn't think I'd love it nearly as much as I did. Hard, and awesome, and far more interesting than previous SaGa games I'd played. And did I mention the soundtrack? I always love a good soundtrack...Kenji Ito knocked this one out of the park.
09 - The Legend of Zelda: A Link to the Past (SNES) -- Not really an RPG, but we cover it at RPGFan, so it makes the list. It also makes the list for being awesome in almost every way.
08 - Final Fantasy VIII (PS) -- The only thing that holds this one back from making the top five is the "draw" system, which is one of the worst gameplay elements ever put in an FF. But seriously, that aside, I love the plot to this game. And I love the art style. And the music. Among Uematsu's scores, I think this one takes the cake for me.
07 - Final Fantasy VI (SNES) / Final Fantasy Anthology (PS) / Final Fantasy VI Advance (GBA) -- So I've beaten this game at least, what, five times? And it's still fun. The GBA port had some added bonuses that I really enjoyed too. The large cast of characters is what makes this one so memorable.
06 - Final Fantasy Tactics (PS) -- I haven't played the PSP version yet (SHAME ON ME!). But even with its poop-tastic translation the first time over (Lich = RICH!), who could forget the job/ability system in its finest hour?
05 - Final Fantasy IX (PS) -- My all-time favorite among the FF series, if for no other reason, because I think it has the most perfect ending among the FF games. If I were to rank FFs based solely on endings, it would be this, then like ... hmmm... X, then XI (Chains of Promathia), then VIII, then throw a bunch together, and put I and XII at the bottom. Man, XII's ending sucked so hard.
04 - Star Ocean: The Second Story (PS) / Star Ocean: Second Evolution (PSP) -- O M F G I love this game. And I am a relative novice with it as well. I STILL haven't picked up all of the playable characters (though I'm attempting to rectify that right now: 'sup Ernest, and new-character Welch). Among Sakuraba's scores, this is the freshest one he's got. Unfortunately, the PSP version cuts the ending FMV that's supposed to play alongside "We Form In Crystals." Now the song is just tacked to a standard staff roll *after* they play the cheesy J-pop song. I miss the crappy CG ending.
03 - Chrono Trigger (SNES) -- I never played the PS or DS versions to completion, so I base my experience primarily on the SNES version, and seeing every single ending (three full playthroughs is what it took for me, though I suspect you can do it in two). I don't really think I have to justify this game making the top three. It's CHRONO TRIGGER. It was fuckin' advertised as coming from the "Dream Team" of developers (basically, Square and Enix a full decade before they merged).
02 - Lunar 2: Eternal Blue Complete (PS) -- For much the same reason as FFIX: a perfect ending. Just, ... man ... totally perfect. Also, awesome music, awesome anime cut scenes, far more interesting (and challenging) battles than Silver Star...the list goes on.
01 - Xenosaga Ep. III: Also Sprach Zarathustra (PS2) -- Hmm... along with being the highest score I've ever given a game on RPGFan (95%), Xenosaga III wins because of Eri Itoh's performance in "Hepatica," which plays in the final T-elos battle. Having soft, sentimental music work in a battle scene is a tricky thing. Mitsuda did it well with "People Seized With Life" in Chrono Cross. But Hepatica certainly won me over. The last...5 or 6 hours of the game, totally unforgettable experience. Also, the nod to Maria and Xenogears in that one part is awesome. Also surprised at how they managed to work in "visit Miltia" in THREE DIFFERENT WAYS throughout the three installments. Oh and uh...also, another totally sweet ending. I'm not even a 2nd-century Gnostic Christian (I'm at least 200% more orthodox than what Takahashi presents in this series), but I love the story.