I'm going to take a stab at giving you a top 5 for the systems I'm more familiar with. A few of them might not technically qualify as a true RPG experience to some, but meh...should still be fun! Some of these would require purchasing repro carts/emulation (unless you can read Japanese). I wont list anything that's impossible to find. Also, if there are remakes, etc of any - I'll match the titles the appropriate system in order to achieve the best experience. You wont find any Zelda games in here, although you should play them if you haven't. Most of the games mentioned before my post are amazing - these are just a few that I've found break the mold a bit (in a good way) and/or come close to perfecting a RPG experience.
These aren't really in order
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NES
1. Sweet Home
2. Destiny of an Emperor
3. Crystalis
4. Dragon Warrior 3
5. Dragon Warrior 4
SNES
1. Breath of Fire 2
2. Terranigma
3. Illusion of Gaia
4. Secret of Evermore
5. Super Mario RPG: Legend of the Seven Stars
GBA
1. Breath of Fire
2. Final Fantasy VI
3. Golden Sun
4. Tales of Phantasia
5. Shining Force: Resurrection of the Dark Dragon
DS
1. Chrono Trigger
2. Dragon Quest IX: Sentinels of the Starry Skies
3. Radiant Historia
4. Shin Megami Tensei: Devil Survivor
5. Valkyrie Profile: Covenant of the Plume
Genesis
1. Phantasy Star IV
2. Shining Force II
3. Pier Solar
4. Beggar Prince
5. Shadowrun
Sega CD
1. Vay
2. Popful Mail
3. Shining Force CD
4. Lunar: The Silver Star
5. Lunar: Eternal Blue
PS1
1. Legend of Dragoon
2. Suikoden II
3. Xenogears
4. Legend of Legaia
5. Parasite Eve
PS2
1. Final Fantasy XII
2. SMT: Nocturne
3. SMT: Digital Devil Saga
4. Shadow Hearts
5. SMT: Persona 4
PSP
1. SMT: Persona 3
2. Star Ocean: First Departure
3. Tactics Ogre: Let Us Cling Together
4. Final Fantasy IV: The Complete Collection
5. Final Fantasy Tactics: The War of the Lions
Since I only did 5 per system, I will point out that some of these systems have so many awesome games that I had to make a few tough decisions. The PS1, PS2, PSP, and DS are extremely RPG heavy. The SNES is has a few others that are amazing as well, and shouldn't be overlooked.