1. Paper Mario the Thousand-Year Door
Funny, witty and looks nice, having jump and various things you can do outside of battle makes it more interesting to play than the average JRPG.
2. Guardian Heroes
It has stats, level-ups, crappy conversations where the various characters use the word "Sword" probably a thousand times ("This is such a great sword! This sword was used in the age of sword."), multiple paths and awesome C&C such as attack the evil guy, three other choices, OR attack the princess you were supposed to save. The basic gameplay works like a side-scrolling beat 'em up game with special moves.
3. Paper Mario
Like TTYD. Also good N64 game that also looks good, what the shit.
4. Pokemon
Grindtastic as shit, but doesn't bother me that much. The plot isn't about saving the world, you just kinda defeat a criminal gang while you're working on your more important goal, becoming the best. I'm not saying the plot is good but I don't dig that emo shit and saving the world from something either. Trying to become a champion at something, now that's a positive attitude. The gameplay is more entertaining than whatever else you'd do at school. The later Pokemon games don't have any reason to still have random encounters and didn't improve upon the formula significantly so they won't appear on this list.
5. Chrono Trigger
No random encounters, no emo characters save for maybe Magus, kick-ass music and it's pretty well paced unlike almost all other JRPG's I have played.
6. Front Mission 3
It's a Japanese game with lots of text boxes, leveling up and combat, so it's a JRPG.
7. Front Mission
Ditto. In some ways it's better than 3, like the plot, graphics, amount of participants in battle, but the upgrading of your mechs is more tiresome and there are only a few battle skills, also the battles practically revolve around missiles only.
8. Super Mario RPG
Funny, better written than your average Bioware game for sure, the graphics and music were awesome at the time.
9. Final Fantasy 7
The music and backrounds are cool, the writing is pretty shit, messing around with materia was fun and there's a sense of adventure. And it spawned the messianic equine Let's Play.
10. Secret of Mana
You could play it with a friend and get into violent arguments over which direction should we go.