Okay, so: I voted for Dragon Quest because it was my first and also the one that I've played the most of the latest installment. (DQ11 was a goddamn delight and FF15...didn't really win me.) Final Fantasy is the obvious second, given that it includes my all-time favorite game (FF4) and I have greatly enjoyed most of the franchise.
I love Breath of Fire, Suikoden, and SaGa; but they all petered out. BoFDQ didn't appeal to me and it kinda killed the series. Suikoden Tierkreis was kind of "in name only" and I'm lead to believe Woven Web of the Centuries is similar. I loved the Game Boy SaGa games and their remakes, but I'm only middling on the later entries in the series. The Lufia series has the same problem--Lufia 2 was the high point, and everything after that has just been trying and failing to get there again. (The Mother series got steadily better, but then stopped.)
I don't put the Seiken Densetsu and Ys series in the same category of games--they're "action rpgs", sure, but so is half the Castlevania series by that definition. I really like pretty much all the entries of both of them, but I don't think of them in the "jrpg" category. Similarly, Fire Emblem is a tactical rpg; it's a different genre, and one I didn't really get into.
I played Tales of Phantasia and wasn't overwhelmed; the same with Trails in the Sky. From Shin Megami Tensei/Persona, I played the first Digital Devil Saga game and Persona 3 Portable and neither of them inspired me to seek out others. Does Xenoblade include Xenogears (a brilliant mess) and Xenosaga (just a mess, and a shameful waste of potential)? I suspect if I'd had access to Phantasy Star as a kid I would have loved it, but I didn't play it until it was well-dated and I didn't have the nostalgia boost.
And if you asked Babywulf his opinion, Pokemon would have topped the charts. He's played almost every game at this point and still periodically asks me if there are any new Pokemon Let's Plays available. (I never really got into it; and I also think that mon-battle rpgs are also outside of the standard jrpg category.)