I'll list some of my ps1 favs, only the ones I can remember haha (and ones that haven't been listed yet I think).
Suikoden 1 and 2 are definitely great games (ps1 games). Suikoden 3 for the ps2, I though was good too, but some look down on it because it doesn't live up to 1 and 2.
While brave fencer musashi isn't a rpg (think its classified as an action game), it was a fun game. I didn't get through the ps2 brave fencer though.
The legend of Legaia, I thought the battle system was amazing back when I played it haha. The story was pretty interesting too, but it kinda jumps forward at the beginning then gets slow somewhere near the middle and then picks right back up.
Legend of dragoon, love dragons and love the timing based combat.
Lunar. I haven't played part 2 yet, but I remember I loved 1 and there were decent singing! The VA commentary at the end was amusing at times too.
Valkyrie Profile. The game was pretty gloomy to me, but I loved all the stories and mystery behind the valkyrie. I believe they remade it for the PSP. I couldn't get into part 2 though.
Saga Frontier 2. Didn't play part 1, but I loved the artstyle of part 2 and the story (even though I can only remember bits and pieces of it right now).
Thousand Arms... just because Ayumi Hamasaki sings the intro... haha, but anyway, it peaked my interests because the combat wasn't pixel art but anime-ish. It was a pretty good game. If I remember correctly, relationship between characters affected forging.
Threads of Fate, more action rpgish/adventure but it was one of the few games my sister actual beat as well.
I'll just dump down vanguard bandits because it was the few rpg (strategy) games with mechas haha (and that was translated).
Oh yeah, not sure about any jrpg pc games. The only ones that come to mind are:
Ys: Good game but its very old.
Magna Carta: Art style by a great artist (although the proportions are weird haha) and the first game was very good. But... I guess this isn't jrpg, because I think its korean, and it was never translated I think (although I think there was a fan translation in the works).