Castle Darkmore, Might and Magic VI probably takes the cake. It's HUGE, filled with enemies that wipe buffs (which cuts your damage output drastically), some enemies can FLY (to make it extra annoying for melee characters), have tons of HP, and worst of all, enemies can cast through walls while you can't. Some enemies also have instant kill spells, if I remember correctly.
It's very fun.
And then there's Wizardry IV, which is one large dungeon and probably the worst in the genre. Many people won't even be able to leave the first room, since you need to summon a specific type of summon (you're an evil lich, you can summon stuff as party members, and hero parties are your enemies) to cast a specific spell on a specific tile - without having the tooltip tell you so - to even find the secret door to leave that room.
That's the easiest puzzle in the game. Other things include teleporters, trapdoors, an area filled with mines you have to trial-and-error through, spinners (that change your direction - did I mention you don't have a map? Gotta draw it yourself), and you also can't really level up, other than finding one-use points that make you stronger ONCE.
It's really brutal. Ah and finally... there's a ghost that pursues you in real time and kills you instantly if he ever catches you. The catch: Real time. As in, if you open the camp menu, and do stuff in there, the ghost is still coming.
Only in a quick look, the games from Atlus, who are the best company in the industry designing complex dungeons, are cited as examples of "worst dungeons".
Atlus? They aren't even close to the best. They're good, but the best? Hardly. If I want complex dungeons, I have to go elsewhere, such as Grimrock. The story focus of Atlus games does take its toll on dungeon design.
