Most numbers are estimates because I have a habit of starting games and then never finishing them so I don't recall how many times I've actually played through a game all the way.
In no particular order:
Disgaea (2, 10+ if you include NG+)
Earthbound (5+)
Final Fantasy Tactics (5+)
FF3 (~5, minus 1 if you don't include the remake)
FF1 (3, 2 if you discount remakes)
FF6 (~5)
FF4 (~3)
DW1 (~2)
DW3 (2-3)
DW4 (10+)
Tales of Eternia (5+)
Tales of Symphonia (2-3)
Wild ARMs 1 (5+)
Wild ARMS 4 (2)
Xenogears (~2? I have several failed replays, though)
Xenosaga (~2)
Seiken Densetsu 3 (~3)
Valkyrie Profile (2)
Vandal Hearts (5+)
SMRPG (~4)
Shadow Hearts (~3)
Shadow Hearts 2 (~2)
Actually, in addition to games that I know I've beaten more than once, here are games I have replayed but never gotten through one of the replays (only games I'm sure of, usually happens 2nd time because I get bored or 1st because the game sucks and I beat it later to bash it):
Fire Emblem 7 (2 times, quit first playthrough)
Fire Emblem 9 (2, 1st)
Final Fantasy 8 (2, 1st)
Final Fantasy 9 (2, 2nd)
Final Fantasy X (2, 1st)
Suikoden 3 (2, 2nd)
Suikoden 5 (2, neither.... what?)
Wild ARMs 3 (2, 2nd)
Wild ARMs 4 (2, 2nd)
Final Fantasy 5 (3, 1st)
Final Fantasy 7 (3, 1st)
Legend of Dragoon (3, 1st)
Pokemon RBY (2, 2nd)
Chrono Cross (2, 1st)
Can't think of anything else. I tend to replay non-RPGs more than RPGs, though, and usually only replay RPGs if they're really good, really bad and I didn't get through the first time, or if I just like the game irrationally.