There was one off-site game called "the dark room" that did exactly that. Not sure where the link is though.
My game "Secrets of the crag" involves a bit of resource management & crafting, though I don't think that's what you mean, as it's mostly focused around dungeon exploration.
Will's "detective" series has a "time" counter that counts down as you gather evidence, is that what you meant?
"The chained god" and my game "ruins of Anzar" have items that need to be constructed and built in a multi-step process.
"Delve" by berka zerka may be a bit like what you meant. It's a combat simulator, and you need to manage all your follower's health and abilities.