There are two main problems with dungeons. The first is that they are unrelated to the rest of the world; when you step into a dungeon, you leave a rich, well-crafted world with interesting things constantly happening for a series of tunnels with nothing in them. Dungeons are microcosms that exist separately from the events of the rest of the game, and that's bad. Did the Black Mountain Clan suck because of those golems that were impossible to kill, or because Arcanum was a game about dialogue and exploration, two things that the BMC abandoned completely. Probably a mix of both of those reasons. Except for whatever item you're in a dungeon to retrieve, it bears no relation to the outside game world, regardless of what a dozen pages of lore will tell you.
The second problem with dungeons is that they are mostly uninteresting. Nothing happens in dungeons except that you kill enemies. Depending on the mechanics of the game you're playing, this can be fun but I'm going to use Arcanum as an example again. Arcanum did not have a good combat system, but even if it did, its strengths were its dialogue and world. The dungeons were bare; nothing happened in them, there was nothing to see or explore. You went from room to room searching for whatever item would allow you to leave, and that is also bad.
One game I played with very good dungeons is Dark Sun: Shattered Lands. One of the first dungeons you go to is this wizard lair in the sewers. It's entirely optional and you don't have to go to it, but it's neat and interesting. When you enter, you meet a rat character who offers to guide you and warns you about the wizard. The rat guy guides you into the lair, where you're introduced to a minor character, the wizard's henchman. As you wander throughout the lair, the rat guy tells you about each of the rooms, what the wizard does in them and what you should look out for. What's really cool is that you can do a couple experiments in the wizard chambers; you can summon oozes if you use the right items or make potions. It's an interactive environment and that's pretty fun! There is one room the rat guy tells you not to enter: a room with a zombie in it. The zombie turns out to be semi-lucid and will follow you. Here's the really interesting part - depending on your actions, the story changes. If you kill the rat guy, he's just a regular rat guy who was trying to help out and kill the wizard. If you get the zombie to follow you after the rat tells you not to, he turns out to be the wizard in disguise. If you ignore the zombie all together, the wizard will kill the rat guy when you confront him. It's a really interesting dynamic that makes it a much more enjoyable experience.
But what can we take from this dungeon? First, the environment is interactive. There are things to do in the dungeon - you can do weird wizard experiments, free prisoners, mess around with this rat guy, free the zombie. Secondly, the dungeon has a story and things actually happen inside of it. Instead of a boring search for an item, you get involved in this sub-plot about a wizard, a rat, a zombie and a crazy henchman. The game always manages to have your attention because something is always happening.
I think the solution is this: blur the distinction between dungeons and the outside world. Instead of having dungeons, have dangerous areas with NPCs in them. Instead of a labyrinthine ruined castle, have a ruined village with a handful of survivors, maybe other explorers, monster inhabitants that you can interact with. Remember New City or that T'Rang base in Wizardry 7 that had monsters in them, but also things to actually do? Maybe a better example is Stonekeep, where the entire game is a dungeon but there are always people to interact with, puzzles to solve and even a town.
Dungeons need to be interesting and well-planned. If a dungeon exists just so you can retrieve an item from it, it probably doesn't need to exist.
Anyway, I just bought Knights of the Chalice. I hope it lives up to the talk!