NES/Handheld:
1. Pokemon RSE (Best of the series? Well, FRLG might beg to differ, but those are minor differences; its still Pokemon at its finest, which is no laughing matter.)
2. Final Fantasy 3 (Very well done game that aged a lot better than you'd expect.)
3. Fire Emblem 7 (Decently polished game and well done overall, for all that I'm not a massive fan of it.)
4. Mario and Luigi Superstar Saga (Pure Fluff game...that did the fluff thing very well, and had actual interesting puzzles! Also, Fawful.)
5. Fire Emblem 8 (FE7-, for the most part.)
6. Pokemon RBY (Pokemon not at its finest! This isn't necessarily a bad thing mind.)
7. Dragon Warrior 4 (One of the better Dragon Warriors, which says more about the rest of the series)
8. Final Fantasy 1 (Considering what it is? Its still decent. Granted, that can only get it so far)
9. Lufia 3 (Bad Dungeons, cliched plot and characters, but the battles are generally fun and the character development (gameplay wise, I just lack a better description) was original and fun)
10. Golden Sun (Utterly generic RPG in like all regards.)
11. Final Fantasy Tactics: Advanced (wait, FFTA got THIS high? This says more about the games below it. Game at least had FFT's gameplay at its heart, even if it was after a chain saw was taken to it.)
12. Dragon Warrior 3 (Tough call between this and FFL2, but when it came down to it? DW3 doesn't punish you for choosing the wrong team on a permanent basis, AND the game is more beatable.)
13. Final Fantasy Legend 2 (Badly polished game, has a lot of the same issues DWs have, in addition to lacking documentation in game that needs it.)
14. Great Greed (One of the worst RPGs I've ever played. Solo RPG that was purely Attack + Heal, humor was some of the worst I've seen, and one of the most boring experiences I've had from start to end. This is a game whose hype will NEVER make sense to me; its absolutely horrid. I seriously can't think of a single redeeming feature this game had, and unlike other titles I disagree with like Xenogears, I can't see it as simply being "it didn't appeal to me", since at best, it thrives off cheap, unfunny humor.)
PSX Era (2 of 2):
1. Valkyrie Profile (Unique RPG that was a lot of fun to play, despite being repetitive. Its no surprise I replayed it several times and enjoyed it everytime I did.)
2. SaGa Frontier (despite its lack of polish, documentation, the game feeling like a Beta, and the existence of RIki's quest, its still a lot of fun with some neat characters and ideas.)
3. Final Fantasy 9 (If this was like 8 years ago when I first played this game, it'd be higher! BUt still a game I liked a fair amount, and the only real bad thing about the game is the horrible load times (it still has some flaws, but I can generally overlook them))
4. Breath of Fire 3 (Solid RPG overall, though the Black Ship arc can still die.)
5. Legend of Mana (Good Sound Track, pretty, and a unique gameplay experience, combined with interesting story in the Jumi Arc. Has its flaws, granted, but this works)
6. Suikoden 2 (ok, starting to notice a drop here. Anyway, game was fun when I first played it...and just gets worse whenever I go back to it. Says something that I started to replay it only 3 separate occasions and only once did I actually get through the entire game.)
7. Lunar:Silver Star Story Complete (Simple and fun game, but not really enough to get it higher, sadly.)
8. Grandia (yeah, really noticing a drop here. Anyway, games not all that bad, but its certainly not that good either.)
9. Wild ARMs 1 (Game pretty much defines average for me on most fronts.)
10. Persona 2 (Game doesn't appeal to me at all. Didn't find the cast as good as hyped, gameplay was dull and boring, dungeons were monotonous...I could go on. Mind, at least the game is PLAYABLE.)
11. Tactics Ogre (some of the worst gameplay and polish ever...but the plot is damned good and the split path idea is neat as well, plus I'll give it brownie points for really being an SNES RPG, and it being creative for its time as a result)
12. Arc the Lad 2 (game was enjoyable...until your team reunited. Then it dropped off so badly to a point where its unforgivably bad. The final boss is also among one of the most retarded things I've ever seen.)
13. Hoshigami (Its Hoshi. I don't think its as bad as some people say it is, but there's no denying the fact that the game is fucking awful.)
NOTE: I'd put Baldur's Gate 2 up here having played a bit of it, but my reasoning for not playing it is not something that exactly counts. Game being unplayable for Hardware or whatever reasons is not something I'm going to hold against a game.
PS2 Era (2 of 2):
1. Fire Emblem 9 (there's a reason this game is one of my 10/10s)
2. Final Fantasy X (Very good on like all fronts.)
3. Star Ocean 3 (FFX, but not quite as good)
4. Breath of Fire 5 (Yeah, game's not as good as I use to think it was, but I still like it a lot)
5. Skies of Arcadia (Just found the game rather decent overall, in most ways, despite its simplicity)
6. Dragon Quest 8 (tough call between this and S5, but the better gameplay and polish (any other DQ game, I wouldn't even CONSIDER that option mind <_<), as well as bonus points for the excellent voice acting put this ahead)
7. Suikoden 5 (Games got some excellent plot and good character work, but...yeah, lacking on most other fronts, and second worst recruitment around.)
8. Final Fantasy 12 (I liked this game though its a pure taste thing, I'll grant. Still came out of it pleasantly surprised)
9. Legaia: Duel Saga (Nice, simple, inoffensive game that's quick to playthrough.)
10. Shadow Hearts (Game hasn't aged that well, though doesn't really feel that bad at the same time)
11. Disgaea (Great characters...and little else.)
12. Final Fantasy X-2 (Battle system showed promise! The plot, characters, existence of Rikku, among other factors did not. Oh, right, it had a decent setting, forgot about that!)
13. Digital Devil Saga (Series) (The "series" thing saves this game cause as a series, DDS isn't really that bad, though DDS1 is still pretty damn meh, and DDS2's gameplay wasn't much better for all that it at least had decent plot and some actual character worth. Yeah, not a fan of SMTs if that's not obvious but its enough to put it above...)
14. Xenosaga 3 (While I don't hate this game as much as others...oh screw it; see what I said about Hoshi? A lot of it applies to XS3 as well!)