A lot of these numbers are going to be fuzzy; I tend to start and not finish replays, for instance, and I don't have clear memories on a lot of them, but.
Roughly ordered by amounts except I don't remember them so expect some blurring:
10+:
Final Fantasy Tactics(....um...I think this may be on ten exactly. Not sure.)
Final Fantasy 6(A dozen or so+the massive amount of time to code Eviltype.)
Chrono Trigger(counting NG+, read down for normal value. I think this is around ten~ not counting alternate endings.)
3-7:
Phantasy Star 4(Not sure on this, but I make it at three replays.)
Earthbound(Believe it or not, I make this at either two or three replays and am not quite sure which. There's like two or three incomplete attempts in there.)
Final Fantasy 4(Two or three. I think it's three. Not counting GBA version.)
Breath of Fire 2(Two or three.)
Lufia 2(Even not counting Retry-which I'm not sure I ever beat, maybe once?-I think this is three or four.)
Seiken Densetsu 3(3, I believe.)
Super Mario RPG(3 or 4)
Final Fantasy 7(3, I thiiiiiink, not certain.)
Legend of Mana(Three or four.)
SaGa Frontier(Six if you see the different mains as replays.)
Chrono Trigger*(Not counting NG+, I make it at four or five replays.)
Star Ocean 2(I had to get down to 1-2 to realize I've replayed this at least three times. *psyduck*)
Super Robot Taisen OG2*(Four replays on NG+. And one on the remake! >_> <_<)
1-2:
Not even trying to recall the amounts here. Just recalling games I've seen the final boss on more than once:
Pokemon Crystal(Yes, specifically Crystal. I've "replayed" Pokemon games by completing the other version, Crystal's the only one I've been through twice fully though, IIRC.)
Shining Force 2
Bahamut Lagoon(I...don't think this was NG+ thinking on it, used a seperate save for...some reason.)
Dragon Ball Z: Legend of the Super Saiyan(shut up I was weirdly bored okay)
Dragon Quest 5
Dragon Quest 6
Final Fantasy 5
Final Fantasy Mystic Quest(I think.)
Live A Live
Magic Knight Rayearth(I think.)
Robotrek
Sailor Moon: Another Story
Secret of Evermore(Technically not. I COUNT IT IF I GET DRUG AWAY HALF-WAY THROUGH THE FINAL BATTLE screw you rentals.)
Secret of Mana
Soulblazer(if it's an RPG, anyways...)
Star Ocean 1
Tales of Phantasia(I thiiiink I played this fully through on the beta, then on the full translation, anyways.)
Paper Mario
Breath of Fire 3(You know, this could be above 3, I am not honestly sure, but I don't think it is.)
Breath of Fire 4(See 3, but more sure it's not.)
Chrono Cross(One full NG+.)
Final Fantasy 7
Final Fantasy 8
Final Fantasy 9
Parasite Eve(Retrospectively I'm pretty sure this is over four of five counting NG+ and counting Chrystler Building as an ending. But I have like two real replays IIRC. Might even be three, not sure...)
Suikoden
Suikoden 2
Super Robot Taisen Alpha Gaiden(It counts if you hack up the replay, right? >_> <_<)
Vagrant Story(Oddly, never finished an NG+, but I've got like one or two replays on it anyways...)
Valkyrie Profile
Wild Arms 2(This may be over 3, don't think so though.)
Xenogears
Pokemon Gen 3*(If you count Pokemon Ru/Sa/Em as the same game, that counts as like two replays, maybe a third, not quite sure if I've actually completed one of my abortive Sapphire runs...)
Super Robot Taisen D*(Once on NG+.)
Super Robot Taisen J*(Twice on NG+.)
Super Robot Taisen OG1(Did both paths fully, one translated one not. I suppose I used the clear save, but that doesn't count with OG1 seeing as how it gives you nothing until you clear both paths.)
Disgaea*(Twice on NG+)
...huh, shorter list than I thought. Hadn't realized I basically have replayed no PS2 games, and how many of my replays I wandered off on. Still good sized, though.