" Back when FFVII was my first RPG experience I remember finding the hardest bosses in the game to be both Demon's Gate as well as Lost Number (the one guarding Vincents vault), the concept of grinding was lost to me and I had to slug it out the hard way. "
Demon's Gate was a tough one for me too back in the days. I remember stopping my first playthrough of the game right there.
From more recent memory, what comes to mind is Prototype and it's last few bosses. The second to last boss took ages to beat, and the last one had a timer counting down.