Inspired by /v/ best cRPG list:
First Tier - Great Games:
Chrono Trigger - The classical jRPG, deserves all it's praise.
Final Fantasy Tactics - Best tactical RPG.
FF VIII, IX or X - Three of the best games in the series, all of them with their charm.
FF XII - A great modern twist, best gameplay in the series.
Tactics Ogre: Knight of Lodis & Let Us Cling Together - Both great tactical RPGs, very similar to FFT.
Disgaea - Great, exotic tactical RPG with humour.
Shin Megami Tensei: Nocturne - Possibly the most loved "non-mainstream" jRPG.
Second Tier - Good Games:
Persona 4 - Best storyfag jRPG ever.
Chrono Cross - "Sequel" to Trigger, tries some wild things and succed in most.
Vagrant Story - Very unique jRPG.
Saga Frontier - Unique game with multiple great stories and kickass soundtrack.
Xenogears - Possibly the most love/hate game on the list, try it out.
Valkyria Chronicles - Great modern twist to Tactical RPGs.
Devil Survivor - Good tactical RPG, blended with SMT monsters.
Pokemon Gold & Silver - Great jRPG, improves the orignal games without becoming a mess.
Dragon Quest VIII - One of the best in the series, bland characters, nice gameplay & exploration.
Breat of Fire 3 - Great game, great characters, you can become a dragon.
Tales of Abyss - IMHO, the best Tales game, storyfag as fuck.
Third Tier - Curiosities:
Super Mario RPG - Solid game, tons of Nintendo fan-service.
Disgaea 2, 3, 4, Phantom Brave, Makai Kingdom, Soul Nomad - Try them if you loved Disgaea.
Earthbound - Funny & solid jRPG, not really that special otherwise.
Kingdom Hearts - If you like Disney.
Odin Sphere - Action RPG, gorgeous graphics and weird story.
Etrian Odissey series - Grind-heavy dungeon-crawlers.
World Ends with You - Bizarre gameplay, fresh take on the genre.
Dark Cloud - Building towns is cool.
Digimon World - I LIKE IT!