In recent memory, it was in Atelier Ayesha against Keithgriff, who you're not really meant to win against, but can if you go in with a lot of patience and a smart setup. I'm pretty sure the fight was like 30 minutes long to complete and got nothing for my trouble other than him claiming to have underestimated me and held back too much.

I remember having to fight for a really long time against the final boss in Mario RPG and it felt like an hour, since it was so long ago I don't know how long it really was, but it took forever to complete.