This is one hell of a question...I'll give my top ten, because any more than that and my post will probably start crashing browsers and people will yell at me.
Asides from the top three, these are in no particular order. The top three have been fixed for years now.
1. Xenoblade Chronicles
I have gushed about this game so many times before, but I will NEVER get tired of it. Xenoblade is perfection. It's not just the best JRPG ever made, it's the best video game ever made, period. It has a brilliantly diverse cast, an amazing soundtrack, an intuitive and engaging combat system that requires your attention constantly, and a story that just won't stop throwing surprises at you even when you're fifty hours in and at the last bloody dungeon. The voice cast is the best I've ever encountered in a video game. The world is massive for a JRPG and exploring every inch of it was something I really wanted to do. Sidequests ranged from the basic to the complex that would affect your relationship with characters - and whether they lived or died in some cases - and there were hundreds of them. It had in-game achievements. The game discouraged grinding but encouraged exploration by giving a lot of EXP for doing everything except fighting monsters over and over, so I saw a lot of the game naturally my first time through.
I love the Monado, too. Seeing visions in battle and stopping them added a level of strategy I'd not seen before in games, and the story visions were extremely misleading - the one on Prison Island, which the game spent hours building up to, did not end the way I expected. Xenoblade did something few games had done: it surprised me. A lot. Bestest game ever.
2. Disgaea 4: A Promise Unforgotten
A Disgaea title was obviously going to appear on my list, and there is no better title than Disgaea 4. It strikes up the perfect blend of political satire and irreverant humour that the Disgaea series is known for, somehow managing to tell a compelling story whilst making a mockery of it. It has a very likeable cast - Valvatorez remains my favourite protagonist in the series to date, even over the power trio of Laharl, Etna, and Flonne - and it offers ridiculously deep gameplay.
I platinumed this on the Vita. It took me 110 hours. I loved every second. Disgaea offers uniquely rewarding gameplay for me in that you're required to spend hours grinding to reach the pinnacle of power, just to beat the game's toughest bosses. Land of Carnage Baal has stats in the billions and can kill you just for coming out of the base. Spending fifty hours or more grinding just to finally kill him is immensely rewarding. This game is all about grinding; no series does it better. You put in the time, you get rewarded with ridiculous (read: trillions) damage numbers. What's not to like?
3. Tales of Symphonia
I've grown disenchanted with the Tales series recently, and part of the reason for that (ignoring the fact that Zestiria was crap) is that none of the titles have reached Symphonia's heights for me. Symphonia took me on an unforgettable journey across two worlds, thrust me into the heart of a conflict that I didn't see the full scope of for over half the game, and introduced me to a completely different type of game. ToS was my first experience with a cel-shaded, more anime-esque JRPG, and as such it's the one I often subsconsciously find myself comparing other, similar games to. I love the battle system, the cast, the soundtrack; all of it. Years later it still looks pretty good on PS3, and the extras made it well worth playing...three times over. This is another difficult plat that I was happy to devote my time and energy to, because I could never get bored of this game.
4. NieR
I have to mention NieR. Most people think solely of the soundtrack when they think of NieR...which is fair enough, because it has the best soundtrack ever; I knew I wanted it from the moment I heard Blu-Bird on the teaser site. But for me, NieR stands out as a truly unforgettable, emotional experience. I had never cried over a video game before NieR. The second ending had me in tears. The game just gets more heartbreaking with each playthrough, as more and more of the world is revealed to you and you go from feeling like a hero to the biggest bastard imaginable.
The game also has some ridiculously dark humour, considering how much of a crapsack the world is. A father out to find his daughter - and we definitely got the better Nier; the younger model wouldn't have had the same emotional impact - joined by a monster boy, a hermaphrodite with an extremely foul mouth, and a very sarcastic talking book. Listening to them talk on the field was disturbingly hilarious. The combat wasn't bad either for an action RPG, and the occasional shake-ups to on-rails shooter, top-down exploration, and even visual novel, were interesting.
...plus the soundtrack. I still can't believe Cold Steel Coffin is a town theme.
5. Resonance of Fate
Resonance of Fate is an unsung gem of the last generation; completely ignored in the wake of Final Fantasy XIII. It's a damn shame, because it's one of the toughest JRPGs tri-Ace have ever put out. The battle system is wonderfully unique yet horrifyingly punishing of even the slightest mistake, reminding me of the days when games punished you for not thinking tactically. Not even by the end of the game are you strong enough to carelessly waste Hero Actions; you are constantly on guard, and one of the game's favourite things is removing party members for a chapter. When you have to go alone with one character, you feel the pressure. In spades.
The value in the story lies more in the chemistry between the three protagonists than anything else. The banter between Leanne, Zephyr and Vashyron is often very entertaining, and their backstories are quite interesting as well. Basel's steampunk setting isn't something you see in JRPGs as much as you used to, and I quite liked the method of exploring it, too - uncovering hexes and connecting terminals for special effects in battle added another layer of strategy and made me want to push through battles for coloured hex drops.
Leanne goes both ways, too. Good to know.
6. Hyperdimension Neptunia.
As a series, because I can't pick just one title. Neptunia is a celebration and a mockery of everything I love about the JRPG genre. It's pure brilliance, no matter what form it takes. The cast are so self-aware (Neptune especially) that you can forgive their blatantly tropified personalities - hell, that is the whole point - and the constant references and one-liners hit the mark more often than not. If ever there was a case for creative localisation, Neptunia makes it and blows all opposing points out of the water, because it's so tongue-in-cheek and tailored specifically for the type of person who will be playing it that you can't not appreciate it. Hell, it even attacks its critics: Nepgear's bland personality in Mk. II was commented upon
by Nepgear herself in Victory, and in an attempt to make up for it she had a bunch of random titles bestowed upon her at points throughout the game. The trophy for starting the game has the description "Think any game reviewers won't get this one!?" attached to it. They hang enough lampshades to power a small third world country.
The combat has also improved in leaps and bounds since the original's abysmal battle system, and they're even making attempts at expanding the story in later instalments like VII, which is as much a visual novel as it is anything else. The series isn't afraid to branch out, either - we've had idol management and action games alongside the standard JRPGs, and will be getting something much bigger in the near future. This series is so ridiculous it defies belief. But it's incredible nonetheless. The new Neptunia game has been the highlight of my year since Mk.II, and I hope it never stops.
7. The Arland trilogy
Atelier Rorona, Totori, and Meruru. These three games stand out for being so unlike typical JRPGs that they're practically in a genre by themselves. Each one tells a compelling, beautiful, and yet extremely relaxed story about a girl trying to make her way in the world - Meruru especially - with a vibrant cast and some horrendously addictive gameplay.
Time management is key in these games, and your skill to manipulate things is far more important than your ability to battle, as turn-based combat is extremely basic and not even that much of a factor unless you're going for specific endings...and these games have a lot of endings. That drive to get the true ending will encourage you to do everything, explore everything, and spend months of your in-game time at the cauldron, mulling over properties and combinations. It's actually surprisingly tense, as it is VERY easy to mess things up irrevocably.
Meruru in particular is my favourite, because Meruru herself changes the most over the game's five years (unless you do literally nothing) and seeing her mature into a confident, charismatic ruler with genuine passions is a wonderful experience. Returning characters are a joy to see - as they've aged some twenty years, asides Rorona, whose lost about that much - and it has the strictest requirements for perfection. The endings are so radically different as well, and seeing Arls develop on the map the more you do is very satisfying.
8. Drakengard
I HAVE to mention this. Find me the most messed-up game you can, and I guarantee that it doesn't even come CLOSE to Drakengard. I wish more games were this irrevocably screwed up. Your casts consists of, amongst others, a mute psychopathic killer, his sister (who loves him and kills herself to stop that from coming out) his best friend (who goes insane and tries to bring her back to life and ends the world in one of the endings), a paedophile priest, an eternally young boy (oh dear...), an elf who eats babies, and a possessed little girl who becomes a fifty-foot fireball throwing monster. I didn't even mention the giant babies with teeth, did I? Oh yes. Asides from the "canon" ending that leads to the second game (the actual canon ending is the secret one, because it leads to NieR) the world ends horribly in every scenario. People die, often in highly justified and cruel ways. It's a complete clusterpsyduck.
Combat is also rather good as well, considering the times. Hack and slash, or blast things to hell with a dragon. It's not the most precise of titles, but there are worse ones out there. The music is something like fifty classical pieces playing simultaneously, and it's pretty long. It's weird. It's an experience. I love it. We need more like this.
9. Baten Kaitos
Ah, Baten Kaitos. I was so excited for this one as a kid. I waited months. Then I got it, and...well. It was everything I had hoped for and more. For one, it was beautiful for a Gamecube game, with amazing scenery no matter where I went. It was also my first taste of Sakuraba's music, so that was a huge thing for me, as I've bought a lot of titles solely because he composed the score for them. The card battle system sticks out in my mind as one of the more unique, well-done examples, as well - it was surprisingly intuitive, being turn-based, yet requiring real-time responses if you wanted to block attacks. Constructing a good deck required a lot of thought.
It was also hard. Psyducking hard. I'm still afraid to go back and try playing it through, because I think I got lucky in finishing it. The trio are easily the hardest bosses I have ever fought. Ever. Then there was Geldoblame, The Angel of Darkness - and holycrap was that a story curveball! - and that bastard awakened Malpercio, who could recover all of his health in a single turn whilst destroying yours...so many temper tantrums over this game. It might just be the hardest JRPG I've ever played. But I have a lot of fond memories of it and the fact that I've never played anything like it before or since make it one of my standout favourites. Baten Kaitos is also a game I owe a lot to; my first forum was a Baten Kaitos one, and I met someone on there I'm still in contact with now, some ten years later. It's a special game for me.
10. Final Fantasy XII
The only numbered Final Fantasy title truly worth playing, in my opinion. I suppose that is a bold claim that others will disagree with, but the thing about FFXII is that it focuses on one thing at the expense of everything else: the world. FFXII is a worldbuilder's dream; it plays out like a high fantasy novel and, whilst that is probably what makes it such a divisive title, it resonates with me more than any other numbered FF title to date. Ivalice is an amazing place, filled with highly empathic, believable characters who aren't all caught up in some godawful tween romance. The godawful tropey romances are gone, and FF really shines without them. Characters are given far more believable and interesting personalities (and yes, I will defend Vaan if called upon to do so) as it doesn't become a case of "good vs. evil" that every other FF ultimately resorts to in some sad bid to keep player interest. FFXII is the only FF with a truly sympathetic villain and, as someone who gravitates towards antagonists this is extremely important to me. Vayne Solidor was a highly complex and fascinating character, and Venat was technically more of a protagonist than the protagonists.
The game also allows you to set your own AI in the Gambit System, and it's as close to real time combat as FF is probably ever going to get as long as it's confined to the slowly fossilising ATB system it so desperately clings to. The orchestral score is sweeping and magnificent and complements the atmosphere perfectly. The voice acting is spectacular, and leaps and bounds above the horribly flat and downright cringeworthy crap FFX gave us - and better than FFXIII's attempt, as well - and it's fantastically paced. Don't get me wrong, other FF titles have their moments. But XII is the pinnacle of the series. XII represents everything FF should be, and it gets a well-deserved place on my favourites list.
...honourable mentions go to The Guided Fate Paradox, Zettai Hero Project: Absolute Victory Unlosing Ranger vs. Darkdeath Evilman, Pokemon Platinum, Star Ocean: The Last Hope, Golden Sun, Tactics Ogre: Let Us Cling Together, and Final Fantasy Tactics: The War of the Lions.
/exhausted from typing all that