The wrinklers are one of the most complicated and interesting features of the game. I've seen a variety of opinions expressed about when to pop them. Pop them all once a day. Pop one wrinkler each hour on the hour, so each one survives for ten (or twelve) hours. In the Wikia it's recommended that wrinklers should not be popped singly; pop them all, or none at all, though the explanation of the rationale is a bit unclear.
I spent some time figuring out the pros and cons of popping wrinklers and came up with a formula. Rather than present the formula though, I'll explain the reasoning behind it:
Exploding a wrinkler incurs a cost, which can be estimated by the difference in wrinkler production from having one fewer wrinkler, multiplied by the expected time for the wrinkler to respawn. In that sense popping a wrinkler is much like selling a building; there is a loss of production as a trade-off for releasing cookies that presumably will be used to buy something else that increases production.
there is clearly no point in popping a wrinkler unless there is something you have in mind to buy with the cookies released. A building or upgrade will increase production by some percentage. By what percentage will production fall due to the loss of one wrinkler? A first guess would be to take the loss of wrinkler production, and divide that by the total wrinkler production. However this gives an overestimate. If (for example) this wrinkler has lived for one hour, but the expected time for replacement by respawning is one minute, the loss is only 1/60 of the above.
My condition for popping a wrinkler is then:
(Lifetime of wrinkler) * (fractional increase in production from object purchased)
> (expected respawn time) * (fractional change in wrinkler production)
There is an additional condition of course: i don't pop wrinklers unless I expect to release enough cookies to purchase the thing I want to buy.
This can do no more than give a rough estimate. I don't note down the time at which each wrinkler appears, so i am just estimating how long it has been there. Also, the "expected time to respawn" is just that - it may be sooner or later.
In practice this means I end up popping all or most of the wrinklers at once. This is because the loss of production is much greater with more wrinklers; there is not much difference between zero and one wrinkler, but a big difference between 9 and 10 wrinklers. As well as that, the fewer wrinklers remaining, the faster they begin to respawn. If it's worth popping one, it's usually worth popping them all.
It also means that I only pop wrinklers in order to buy expensive upgrades and high buildings. Normally it's only prisms and antimatter thingies. For anything smaller, it's generally better to just let existing production continue until I have enough cookies to cover the cost, which won't take very long.