Most recently produced JRPG that I played was Final Fantasy X, so I am at a bit of a disadvantage. However, if you don't mind sprites, Final Fantasy VI is a rather good game. Interesting characters, good story, a memorable villain, etc. Gameplay is clunky by modern standards, and has a couple of notable gamebreaking exploits, but the story more than makes up for it. Strongly recommended.
Others:
Chrono Cross
Chrono Trigger
Final Fantasy V
Final Fantasy VII
Kingdom Hearts
All of my favorites were produced by Square Enix for some reason. The quality of rpgs that they have been producing recently saddens me.