1. Final Fantasy series (All of them)
2. Tales of
3. Kingdom Hearts series
4. Lost Odyssey
5. Star Ocean (Series)

1-Dark souls
2-Demon souls
3-Chrono Cross
4-Final Fantasy X
5-Persona 4

It's so hard I know the act of listing those five games will make me start to remember many more that are equally deserving of a top five spot . woe is me.
no particular order
Persona 4 golden
Shadow Hearts covenant
Parasite Eve
Final Fantasy 7
Vagrant Story

Besides the ones you listed, Paper Mario (N64, GCN ones).

Yesssss!

Top 5:

1) Suikoden (Amazing series, but 3 is my favorite)
2) Final Fantasy (VI is my favorite)
3) Legend of Dragoon
4) Chrono (Both Cross and Trigger are fantastic games)
5) Shadow Hearts (The second game is a better game, but fuck did the first one just WOW me out of nowhere!)

I do not count Demon's Souls / Dark Souls as JRPGs or they would be here.

let's see, xenoblade is a new amazing franchise in the genre, there's also paper mario (the first two wich are the only real ones), fire emblem, POKEMON, final fantasy tactics, tales of series (symphonia recommended to the extreme). the list goes on and on.

UHmm, I haven't made up my mind but the top 5 should include:
-Lufia
-Chrono Trigger
-Final Fantasy IV
-Final Fantasy VI
-Pokemon Red/Blue

If we add, S-RPG made in Japan the thing gets complicated.

I still need to finish Xenoblade, Dragon Quest IX, and Final Fantasy III (but probably this won't make it to my top 5), and I just got Ni No Kuni and a Golden Sun one.

Not franchises...

1- Final Fantasy VI
2- Chrono Trigger
3- Xenogears
4- .hack -G.U. Trilogy- (treating all 3 games as a whole)
5- Persona 3
6- Phantasy Star IV
7- Shin Megami Tensei 3
8- Suikoden 3 (III)
9- Kingdom Hearts II
10- Pokemon (main saga)

1. Chrono Trigger
2. XenoBlade Chronicles
3. Skies of Arcadia Legends