I'll third the Dark Elf Cave, that place made Cecil practically useless forcing me to rely on weak, underleveled characters.

Speaking of tedious places, Dark World in Final Fantasy III was simply impossible, had to beat four though opponents just to make the last one a little bit easier, and all that with no save point in sight.

The caves in Final Fantasy Dawn of Souls where you get to fight the optional bosses were just annoying, not really the bosses as the time it took to reach them.