Not exactly "dungeon" themed but you might wanna give Majesty and Majesty 2 a try.

In the Majesty series, you don't control directly your units. You choose what to build, what to research. Your heroes are then buying stuff from your marketplace, your forge.

The only control you have over them is by placing "quests", to attack enemy lairs, or defend your own buildings. But most of the time, they will just act on their own, go for exploration, or fight enemies on their own.

The villagers, guards, and tax collectors are completely autonomous, and care about your buildings, without you giving an order.

Recently has been announced the game Dungeons ^[1] (no official site for now, to be edited later).

It is meant to be the spiritual child of the Dungeon Keeper series, only without the license.

You can read more about it on the Rock Paper Shotgun article ^[2].

Startopia ^[1] could answer the need as well, though it's not placed in a "medieval dungeon" setting.

Made by former Bullfrog employees (makers of Theme Hospital and Dungeon Keeper), this game puts you in command of a donut-shaped space station, in charge of building and arranging it so that your alien visitors can have a nice time. You can hire some of them to work at your facilities, but that's almost all the control you have over them.

It plays in a similar way to Theme Hospital and Dungeon Keeper.

Goblin Camp ^[1] is a game inspired by Dwarf Fortress and Dungeon Keeper, in which you have a camp of goblins and orcs to manage.

It is close graphically to Dwarf Fortress, with the difference that it proposes a mouse interface instead of keyboard shortcuts. You can check this video ^[2], to get an idea.

www.dungeonquestgame.com - This contains source code, but I believe there is a level editor too. It is written in C# and XNA.