I'd like to see 'clearable' monster lairs.
The lairs would spawn monsters until you physically go in and clear them out. Using whatever 'spawning' formula is appropriate.
Finding them would probably involve moving into the lair square. You'd get a dialogue stating you'd found the lair entrance, and it would ask you if you'd like to enter...
Even if you chose not to enter the lair at that time, there would be a chance of an immediate encounter, because you've run afoul of the lair guards.
Tackling lairs would be difficult, i.e. you'd need to face a LOT of monsters at once.
Obviously, lairs of the 'lesser' monsters would be easier to clear out than the tougher monsters.
Successfully clearing a lair would 'shut it down' for a number of turns, and upon successful clearing of said lair, you'd be able to raid the lair treasury, perhaps finding an artifact or magic item(s) along with the gildar reward.
New or recently reactivated lairs would become stronger over time. So, if a recently cleared lair has just become active, that would be the best time to clear it out. With this in mind, you might want to station a sentry/guard post near a cleared lair to keep an eye out for trouble.
If a particular monster is a 'resource' for your kingdom/empire (say Darklings, Spiders, or Wargs), perhaps you could discuss an 'alliance' with said lair instead of clearing it, allowing you to hire 'mercenary' monsters.
To make things more interesting, any monsters from a lair who successfully sack a nearby city would increase the strength of their own lair, and maybe add some gildar to their horde as well.