SNES Era:
1. Tales of Phantasia - Game feels like the quintessential ARPG, loved it back when it was first fan translated. Still enjoy the story and characters.
2. Final Fantasy 6 - Game feels like the quintessential RPG. Played this so many times. Still love playing it. The story still holds up to modern games, and outshines quite a lot of them.
3. Phantasy Star 4 - Classic JRPG done right. Fun, yet straightforward, battle system. Cliched, but charming, characters. Fantasy/Sci-fi setting caught my attention.
4. Earthbound - Because funny matters.
5. Super Mario RPG - Quite a few laugh-out-loud moments in this game, plus solid timing mechanics battle system.
6. Final Fantasy 4 - Classic, the newer translations save this game, which was otherwise only 'good for its time'. Gets points for being hilariously melodramatic.
7. Chrono Trigger - Polished JRPG. Fun team attack system. Enjoyed the Time Travel story.
8. Breath of Fire 2 - They polished BoF1 until it was fun. Story is lacking, but characters are more enjoyable this time.
9. Lufia 2 - Really enjoyed its unique-for-the-time gameplay mechanics.
10. Final Fantasy 5 - Job system whee! I actually even enjoyed the story here.
11. Ogre Battle - Felt clunky, but I have nothing against it. Did some neat things with the RPG/RTS genre, suffers from age and an 'unfinished' feeling.
12. Breath of Fire 1 - Just... wasn't very fun. Nothing horribly wrong with it, just bland.
13. Shining Force 2 - Another bland game, though not bad.
PSX Era (1 of 2:
1. Final Fantasy 7 - Overall solid on story, characters, and gameplay, feels deserving of the top spot here.
2. Star Ocean 2 - Really liked the setting, gameplay, PAs, and characters. Double-main characters are still a nice touch, even if Rena's story is nerfed.
3. Lunar: Eternal Blue Complete - Because a good translation matters.
4. Suikoden 1 - Unpolished, but still an auspicious start to a great series.
5. Tales of Eternia - They built a faster ARPG and tried a little harder at the story (though failed in that department). Still fun to play, so it gets high marks.
6. Breath of Fire 4 - A BoF game where I care about the story? High marks!
7. Wild ARMs 2 - Feels unpolished, but overall average.
8. Final Fantasy Tactics - Polished, good characters/story - but absolutely puts me to sleep, inexplicably boring in every way.
9. Final Fantasy 8 - Pretty character designs is about all this has going for it.
10. Vagrant Story - My hatred for this battle system knows no bounds and thusly, it is sub-FF8.
11. Chrono Cross - Played this so many times, yet I still can't bring myself to rank it any higher.
12. Dragon Warrior 7 - Fail? No. Utter Fail.
PS2 Era (1 of 2)
Disgaea 2 - Great on all accounts - well-told story, finely-tuned gameplay, humorous dialogue and gameplay mechanics, likable characters. Not without some flaws, but I'd rank it above everything here.
Suikoden 3 - Another solid game that keeps on giving. Great story, even if it lags at times. Memorable characters and a memorable setting. Still the most polished Suikoden gameplay system.
Wild ARMs 4 - Gameplay! Best use of platforming in an RPG. Hybrid battle system is great, and each character fills their own role in battle. Villain cast is a happy collection of supervillains out of a DC comic book, but with fun anime touches on them. Story moves at a nice pace, and while the twists are predictable, they still play out well and with great excitement!
Odin Sphere - Shakespeare-style soliloquy complete with spotlight is a storytelling device more RPGs should steal. Both hilarious and interesting to see in use. The game feels more like the latest evolution of the side-scroller rather than an RPG, but it does what it does well, and it deserves this spot for its inventiveness.
Valkyrie Profile 2 - Truth be told, I liked the fanfiction-esque storyline here, and the SRPG/ARPG hybrid battle system was just great icing on the cake. Also, the game has Arngrim, which would merit this spot on its own. Yes, I'm a bit biased on that point.
Shadow Hearts 2 - The highlight of the Shadow Hearts series. I have no complaints about this game, only praise for its good points.
Tales of Symphonia - As an ARPG fan, ToS was a treat - effective multiplayer ARPG battles are always fun for me. Additionally, the cast had good chemistry, and the laundry list of JRPG cliches felt like a love letter to traditional fantasy RPGs and ToP in particular. Also, Zelos!
Wild ARMs 3 - Cast had good chemistry, the story came together nicely. Gameplay was boring and slow, and the puzzles irritated me. Average.
Wild ARMs 5 - Overall average gameplay, average cast, but not quite as good as WA3's cast.
Kingdom Hearts - I love crossovers, but don't like playing this game, so it evens out.
Shadow Hearts 3 - Still a SH game, so it's not bad, but it's just nowhere near as good as SH2.
Xenosaga 1 - The least offensive of the XS series, still haven't finished XS2 or started XS3, though. I didn't hate this game, but it's the lowest on this list.
Radiata Stories - Except for this game, which is not very fun to play at all, and the biggest disappointment from Tri-Ace in my opinion. Ridley and Jack were a good pair of characters at least. I still want to see Jack ranked, despite how little I liked the gameplay of this game.
-Djinn