It's really hard to remember them all and opinions change with times and relative to other games, but here goes:
Final Fantasy:
1 - Pretty good 2 - OK 3 - Pretty good 4 - Great 5 - OK, job system is great 6 - Masterpiece 7 - Masterpiece 8 - Not good 9 - OK 10 - Terrible, battle system was great, story/characters complete train wreck 12 - Terrible, felt like a boring mmo, forgettable 13 - Terrible, battle system was somewhat interesting at times Chrono:
Trigger - Masterpiece Cross - Great
Suikoden:
1 - Great 2 - Masterpiece 3 - OK 4 - OK 5 - OK/Good
Pesrona:
1- Not good 2 - Pretty Good 3 - Great 4 - Great (could be a masterpiece, but a lot of things bring this game down IMO and might be most overrated game I love)
Ys:
Origin - Great 1 - OK 2 - OK 3 - Good 4 - Good 5 - Good 6 - OK
Mana:
Final Fantasy Adventure - OK Secret of Mana - Great Sieken Densetsu 3- Masterpiece Secret of Evermore - OK Legend of Mana - OK Sword of Mana- Good
Dragon Quest:
1 - OK 2 - OK 3 - Good 4 - Very Good 5 - Great 6 - Good 7 - Great 8 - OK 9 - Great
SaGa:
1 - OK 2 - Good 3 - Good Frontier - Bad Frontier 2 - Terrible
Wild Arms
1 - OK 2 - Good 3 - Great 4 - Bad 5 - Bad
XenoSaga
1 - Great 2 - Bad 3 - Great
Golden Sun:
1 - Great 2 - Great 3 - OK
Disgaea:
1 - Great 2 - Masterpiece 3 - Great
Kiseki :
Sora no Kiseki FC - Great Sora no Kiseki SC - Great Sora no Kiseki The 3rd - Masterpiece Zero no Kiseki - Great
SMT/Etrian Odyssey/Tales/Others:
I don't remember well enough to rate this fairly, but I have fond memories and a bunch of the related games in my queue. I'd rate as a series, SMT as great, Etrian Odyssey as great as long as you know what you're getting into, and Tales as OK.
Overall, my favorite long-running series that have withstood the test of time are Dragon Quest and Final Fantasy. For modern and new RPGs though, I mainly prefer things published or written by Atlus such as Persona or SMT series, but I should also include the Kiseki series.