Had a discussion about using cards for random encounters the other day and it reminded me of my old trouble queue proposal.
Thinking about it further, using a deck instead of a random encounter table seems like a really good idea. Roll up a bunch of random encounters beforehand, say one per two empty rooms in the level (so probably 10-15 encounters, which should be more than players will meet in any single expedition). Put each one on a notecard. Whenever you roll a random encounter during exploration, draw the top notecard off of the deck. If the PCs kill it, don't return it to the deck, and if they flee from it, update it (remove anything killed from it, say) and return it to the deck.
So then the deck represents a set of facts about the world: it's the set of small groups of monsters without rooms in the dungeon level.
Between sessions, restocking the dungeon means refilling the deck. The simple, obvious way to do this is to roll up more random encounters from a level-appropriate table, put them on cards, and add them to the deck. But you could do a lot of interesting procedural stuff with this too. Maybe you draw a couple of times from the deck and the random encounters that you drew take an action on the deck. Humanoids might invite their cousins, adding another random encounter of their type to the deck. Maybe predators like giant spiders remove a card of a prey species type from the deck (or are removed themselves if no prey cards remain). Undead might take another draw and turn that into an encounter of their type (or you could animate encounters cleared by the PCs and add them). If you draw a rival adventuring party, draw again and they fight whatever you drew. Maybe if you ever have four random encounters of a single kind in the deck at restock-time, they form a lair, removing them from the deck and adding them to the map. Likewise, if the PCs knock over a lair but there are survivors, maybe they get added to the deck as encounters. It all seems like a relatively low-overhead way to add some liveness to the dungeon's inhabitants.
And if you have your random encounters on notecards, this seems like a good place to store the state of your named beastman champions, including two or three words of personality description and any permanent injuries or magic items they might have gotten from previous PCs. You could even leave lairs in the deck; if a lair has six encounters, then you have six cards, and each card says "part of lair x". So then your players can wage a war of attrition, trying to destroy the lair piecemeal rather than fighting it all at once (but likewise, those encounters have somewhere to retreat to and if they get away may bring reinforcements).
And then bringing it all back around, if your players have caused trouble and there are impending consequences that might reasonably find them, you make a card for it and shuffle it in to the random encounter deck of wherever that trouble is looking for them. Maybe mark cards as "global trouble" vs "level inhabitants" so that they're easy to separate for shuffling into another area's deck.
... now the only problem is that I don't actually own any notecards.