Chocobo Hot and Cold for me as well. Cid said it best about what makes it so great - it’s varied and actually rewarding.
Chocobo Hot and Cold is up there, but I did like that little shell-shooting minigame in Super Mario RPG you get in the Mushroom Kingdom.
I really liked the lightning dodging game from FFX.
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Seriously, Dragon Quest poker (even my mom liked that, so I got her to get coins for me :D), Triple Triad, and the archery games from Zelda:ALttP and OoT (horseback archery!). Chocobo Hot and Cold was a lot of fun too the one time I played FFIX.
Lightning dodging was no problem for me. Made it to 200 bolts easy. However, I didn;t bother with, say, Blitzball. Or the Monster Arena (techncially not a mini game, but close enough.) I think it’s safe to say i enjoyed FFX a lot mroe BECAUSE I didn’t bother with msot of the optional shit.