If optional dungeons are allowed to be counted... The Hall of Darkness from Etrian Odyssey IV takes the cake, literally every monster there qualifies as a Demonic Spider. I had to plan for some enemy formations as if they were just short of boss fights. AoE Petrification mobs in that always come in groups? check. High power AoE physical attackers that can two shot the party AND support mobs with extreme evasion lurking behind them? check. Mobs that become powered-up berserkers if an ally falls? check. F.O.E.s that operate as packs? check. Blackout rooms, ice puzzles, and hidden damage floors? check..... well trout, now that I think of it I never got around to killing the Superboss there.

For story required dungeons there is the Great Underpass of Ginza in Shin Megami Tensei: Nocturne. There are no doubt worse but I remember this one purely because it was stand-out obnoxious. Realized a little late it was basically a Marathon Level with multiple blackout rooms, damage floors, hidden pits, and combinations of the three.... oh, and a random encounter mob that can use Beast Eye to give his group extra turns. Worst detour ever, but at least it was entertaining.