dungeon construction: organisation

The occupants of a dungeon have their own social and ecological hierarchy. While such considerations are seen by some as getting in the way of fun, a couple of quick yes/no questions and some light thinking about who would live in a dungeon like yours can go a long way to making a dungeon distinct.
At most, do what players will encounter (you have an enclosed environment after all) - avoid bogging down in campaign history and remember, history is written by the winners so a few sins against conventional knowledge are allowed - after all, you weren't there man! Ahem.

Who built it?
Someone wanted your dungeon to happen. They went to the effort of arranging for tunnels to be carved or occupying caves (unless your architect is single-minded, has extraordinary capabilities or is some kind of tunnelling freak) and preparing areas for habitation. This architect has a name and personality, infused the dungeon with character and had to deal with the elements involved in making a place like this. This is a non-player character (though an amnesiac player character would be a nice twist) or group with money, determination and resources. Knowing who this is will be helpful and can inform the dungeon's character and history.

Who's in charge?
This need not be the architect. This may be a single individual or there could be a number of leaders vying for control for a piece or for the whole pie. There are leader-types in many games, these command their forces using various methods (like bribery, threats or magic) or may have a more insidious relationship (parasitic perhaps?) with their lackeys. Players may have to come up with strategies to break the chain of command or may decide to challenge the leader to a duel in order to minimise the number of deaths. They may even know the original architect or sing songs about what they'd do to them...

Who's on top?
Say you're a orcish berserker. You know there's some wussy goblins upstairs who have some nice trinkets. Do you go up there and take it from them or do you let them mock you with their new-found wealth? Is there a tribe of lizardmen who bring the dragon nesting in their lair gold and other treasures? This need not be just about wealth but also about food - the biggest predator will likely dominate an area unless those beneath it can somehow defend themselves. Player characters are not the only ones who kill dungeon inhabitants after all... Those who have the power can determine their role within the dungeon or may even seek to escape it's confines.

Who's at the bottom?
For every power, there's bootlickers, lickspittles and sycophants. Particularly where largely evil populations congregate and lair, there's someone who toadies up to the leaders or who becomes a pariah through weakness, cowardice or excessive evil (even murderers may not like the idea of a serial killer being next to them) and this may lead to variations in populations. In food terms, think of scavengers and other lowly creatures as well as those creatures who are the primary food source. Someone may pick at the bones of the dead (those that aren't moving of course) and these scavengers are not even forced to be giant ameobae, vultures or insects.