1. Pokemon Gold
2. Kingdom Hearts II
3. Kingdom Hearts
4. Pokemon red
5. Pokemon blue.

Now in fairness, the canon of genre classification is necessarily going to change over time, especially with a medium that's had as little serious critical analysis as video games have had.

That said, the genre classifications as they exist right now are pretty iron-clad, and that's not going to change unless the people who want to change it become part of the literati dialogue groups.

1. Paper Mario
2. Pokemon Emerald
3. Final Fantasy IV (DS)
4. Pokemon Diamond
5. Super Mario RPG

I haven't played that many JRPG's

I hope they change eventually.  Change would be good... though I was a bit sad to see Adventure practically get replaced by aRPG.

My Top 5 favorite JRPG's are:

1) Final Fantasy X
2) Kingdom Hearts
3) Kingdom Hearts 2
4) Pokemon Yellow
5) Pokemon Silver

1. Arc The Lad: Twilight Of The Spirits
2. Final Fantasy 9
3. Paper Mario: The Thousand Year Door
4. Golden Sun
5. Final Fantasy 6

My top five would have to be

1) Suikoden 5
2) Tales of the Abyss
3) Star Ocean 3
4) Grandia 2
5) Skies of Arcadia