The Tavern

some form of clock may be considered necessary, because of how monster wandering works, to prevent behavior like waiting forever for monsters to come to you, a form of scumming which the interface makes very easy. But as in many other games, I think it should be something not even noticeable if one plays normally. It should just make smartasses first go "hey, why don't I just...", and 1 minute later go "ohh... that's why. K, nevermind."

temporary drain/decay over time

sipmly inflict a small amount of Drain all the time, flavored as getting rusty, perhaps capped to some amount. This has all the advantages and disadvantages of any XP-gated mechanic. Drain is almost everywhere these days; maybe we can get on with it and actually have it everywhere. Piety decay may be considered a variant of this.

irreversible drain/decay over time

permanently losing skills would be bad because it essentially allows re-skilling (which is an Ash power) and makes you frequently check that your skills are where you want them to be. This could be done without permitting re-skilling, by setting up a constantly increasing skill point deficit that must be set to zero before skill points can train skills, but that is ugly and hard to communicate. A nicer type of irreversible drain is to constantly reduce the player's XL, and is a mechanism I favor. For example, every XL*10 turns, remove 1% of the player's progress to the next level. This punishes backtracking, but autotravel is rather efficient with backtracking, so unless one stashes a lot (which can be fixed with other overhauls) it's not really a big issue, at least compared to autoexplore's inefficiency. But even autoexplore wastes less time than you spend resting, if you're a normal kind of player and character, so I don't believe it would make many people stop autoexploring.

increasing disadvantage restricted to a level over time

you can give players some kind of malus that increases the longer one spends waiting on a level, but then you encourage weird behavior: it's best to rest off the level you're clearing, i.e. go downstairs, find and get into a fight, go upstairs to rest, repeat. It is a natural problem for characters who tend to rest a lot, like conjurers. There's no good reason to make players avoid resting on uncleared levels beyond the already-present threat of wandering monsters.

increased/intensified monster generation over time

as a form of the previously described clock, this is unfortunately a mixed incentive because generated monsters give experience/items/piety, so it has the opposite effect by encouraging scumming. Making newly generated monsters essentially durable summons is not a good idea because knowing that you're not getting rewarded for killing is a real turn-off because it makes the killing feel pointless.

mark, god wrath, level destruction, doom machines, food

these clocks are not simple to analyze and obscure basic questions like
should time pressure be something you can set back to 0 and fully recover from, by acting in a timely manner for a while?
should the clock be restricted to a level/branch or carry over between levels/branches?
should it kill the player or just make progress harder?

I'd be down with a food clock like in Rogue (no corpses), that gave sufficient nutrition you'd only have to hit 'e' once in a great while, and no interaction with abilities or spells.

The problem is conjurations are built around mashing 5 after every small fight, and that uses up a lot of food.

Just make the food clock extremely generous, get rid of chunk eating, and get rid of hunger costs for spells and abilities. This will essentially be equivalent to no food clock for normal players, while preventing hypothetical optimal players from spending 100ks of turns per floor to get monsters on to optimal terrain for a 0.00001% better chance to win, or whatever it is they're supposed to do. Design purity is preserved, while leaving the status quo the same for normal people and reducing annoyance from butchering, travel interruptions from hunger, and so on. I think this is a pretty simple solution, but not overly interesting.

Give nutrition upon entering a new level (with a message about eating or something for new players). Why have food items if the clock isn't a clock? Actually why have the system when it doesn't even stop people from scumming as-is?

If you got rid of chunks then the food clock would stop scumming reasonably well.

If going down this path, next step would be to "goldify" food and get rid of the distinction between food and satiation. You would have a steadily decreasing meter that kills you when it hits 0. Picking up food would add so-and-so many units to the meter. But if starvation mattered in someone's game, it would be more interesting to have it be based on exploration (necessitating a re-flavoring) than on finding an arbitrary class of items, because then the player would have some clear (if dangerous) way to manage the crisis instead of just dying to stingy food drops.

Another possible "clock" is to just remove all monster generation after level creation. This makes any sort of strategic scumming (i.e. maximizing XP, or anything dependent on it) impossible, but makes certain types of tactical scumming easier (since you know cleared levels are absolutely safe). Letting monsters cross staircases, Brogue-style, would help with the second part.

Another interesting clock would be a mutation clock. The player has been infected with numerous germs from uncountable enemies down the dungeon, and also the dungeon has background radiation which is the reason rats and bats are enemies at all, for example. The more time you spend down there, the more random mutations you adquire. There's no chance to cure them via potion or Zin and you can't resist them, like if they were intrinsic to your race. Also, they don't have to be "Bad mutations", just a random permanent mutation like Tier 3 Hooves is enough to annoy the player a bit.
Problem is, this would mess with 15 rune games, so the clock would have to be implemented around runes (do you know what I mean?), let me give an example because I don't know the numbers:

At the start, you are given 50000 Turns to adquire your first rune. (Imagine any amount of turns you want, I'm not a good player so I don't know what would be reasonable) If 50000 turns pass, the player adquires a random intrinsic mutation. So, if you pick the rune, the turn count resets. Here's the thing: Every time turn count resets via mutation the amount of turns required is reduced by a permanent amount, like 20% or 30% (40000 or 33000 turns in my previous example).
Oh, and this clock would stop running overall while in Ziggurats.

Do you guys think this could be a thing? I gotta go now but if I come back and you think it's reasonable and healthy enough for the game, I'll make a detailed thread with my idea because I ran out of time.

Adom has that. Certain (deeper) areas of the game have background corruption and after 90 days of game time have passed, the corruption rate doubles. When you become more and more corrupted you will receive (mostly) harmful mutations.

In practice this does not actually matter, there are plenty enough sources for removing those mutations in the game. All my winners (mostly ultra endings) took their time with no rush.

Disclaimer: I haven't played Adom in years so no idea what's the current situation.

The thing I suggested was intrinsic mutations. The player won't be able to remove those mutations in any way