I'm pretty sure I posted in this thread a ways back, but I've play some more titles since then, so I'll post again.
In no particular order:
3.Persona 2 (Both Innocent Sin(thanks to the translation patch,)&Eternal Punishment.)
4.Arc the Lad II.
5.Dragonquest V (DS)
Some info on those last two; firstly, they are possibly my least favorite of all my favorites, but I still count them on the list. Secondly, these are both freeware titles, made by the same guy. Naturally, the production values can't compare to commercial games, but the titles themselves underneath all that; I thought they were rather good, containing everything that draws me to the genre, and doing it well. Exit Fate in particular is a Suikoden homage, (more-so of II,) and even uses tilesets from and has a similar spriteset to it, so you can see why I'm fond of that one.
Oh, and 8. The Laxius Force Trilogy. Independent RPG's made with RPGMaker; read the reviews here if you're interested. Like those last two, it's the least of my favorites, but I really like it/them anyways, despite production values even lower than Last Scenario.
Honorable Mention: Chrono Cross. For a while, it did seem like would end up being something real nice, but it ultimately turned into a mess by the end.
And finally, while I'm far from finished with Legends of Heroes: Trails in the Sky, it may well end up being one of my top favorites.