Ogre Battle 64 is the ONLY game that I've replayed this many times with the exception of Chrono Trigger (but that was back when the only RPGs I'd ever played were FF4/6 and CT).
The only other rpgs I've gone back after full completion and played through again were (listed in order of favoritism)
1. Valkyrie Profile Lenneth
2. Growlanser 2
3. FF Tactics
4. Grandia 2
5. Chrono Trigger
Out of any other single player games, I haven't found anything else worth playing beyond getting the full completion. Those first two listed along with OB64 and Disgaea 1 and 2 are my favorite RPGs. I can't list Disgaea 1 or 2 in the repeated plays because every time I go back to play them more, I'm just grinding out more stuff to work my way to an ultimate file (never gonna happen).
Magnus - Can't say I'm a big fan of the Mana series. That sort of gameplay never really was my thing, I guess. I'm not a fan of most action/rpg hybrids.
Mightwish - Original megaman games are too hardcore! I can't handle them. Too much hard platforming, and that just ends up either frustrating me or boring me. I'm a much bigger fan of the MM Zero or ZX series, which have a stronger emphasis on action over just platforming. I have mad respect for those who can play through those older grueling platformers though.
Caiooa - I like Ogre Battle 64 over March of the Black Queen because of the massive improvements to the engine. Selecting units, precise movement, being able to tell exactly when you're going to initiate battle with an opponent, they're all made so much easier to deal with in the 64 version. It really makes the game have much less little annoyances and allow you to enjoy all the good points more. That's how I felt about it anyway.
Ultima and Hasuko - I don't really count puzzle games for the same reason I don't count fighters, shmups, or party games. They're meant to be replayed endlessly, so it's only natural to go back to them again and again. Also Hasuko, somehow I end up referencing into Altered Beast on a near-daily basis. I have way too many fond memories of that game. It's a shame my copy got stolen back in the day.
Crosseyes - OG Donkey Kong! Was the game boy version of that the same as the original NES version? Cuz that's the only one I've ever beaten (which is a feat for me, since platformers aren't my thing). That shit had some crazy puzzles in it though.
Shin - You know, I have both lunar games, but I haven't played much into either. I wanted to finish the first before starting the second, but the first one makes me ragequit early on every time. lol. It's pretty sad. I hear Lunar 2 is leagues better and that I should just skip to it, but I can't help but want to play them in order. And holy fuck, that's too many games to go back and replay for me. Generally speaking, I'd much rather move on to something new than go back and play through a game I already know everything about. It takes a lot for me to want to play through a game purely for its story, because I remember everything about it too well as I replay through. It's like...watching a movie and having someone spoil everything a couple minutes before it happens, you know? Also random note, I always wanted to play Skies of Arcadia. I heard it was great.
Vhaeraun - Man, those Tales games always leave me feeling disappointed. I look at the battle system and envision how they could make small improvements to add so much more depth, and then I get sad and stop playing. Eternia was good, and from what it looks like Destiny 2 seems even better, but it still just feels too lacking in the battles. This is why I can't play action/rpgs. They always feel like they just half-assed the action and the rpg and shoved them together to try and make a whole. I can't be satisfied with something like that!
GLZ - RE4? That's a pretty strong testiment to the quality of the game. I'd heard it was very good, but I'm honestly surprised. I'll have to make a real effort to get it and play it through.