Best way to slow down a thread? Is using Sleep() OK?

Why don't you use a lower priority for the calculation threads? That will ensure other threads are scheduled while allowing your calculation threads to run as fast as possible if no other threads need to run.

What is wrong with the CPU at 100%? That's what you should strive for, not try to avoid. These math calculations are important, no? Unless you're trying to avoid hogging some other resource not explicitly managed by the OS (a mutex, the disk, etc) and used by the main thread, generally trying to slow your thread down is a bad idea. What about on multicore systems (which almost all systems will be, going forward)? You'd be slowing down a thread for absolutely no reason.

The OS has a concept of a thread quantum. It will take care of ensuring that no important thread on your system is starved. And, as I mentioned, on multicore systems spiking one thread on one CPU does not hurt performance for other threads on other cores at all.

I also see in another comment that this thread is also doing a lot of disk I/O - these operations will already cause your thread to yield while it's waiting for the results, so the sleeps will do nothing.

In general, if you're calling Sleep(x), there is something wrong/lazy with your design, and if x==0, you're opening yourself up to live locks (the thread calling Sleep(0) can actually be rescheduled immediately, making it a noop).

Sleep should be fine for throttling an app, which from your comments is what you're after. Perhaps you just need to be more precise how long you sleep for.

The only software in which I use a feature like this is the BOINC client. I don't know what mechanism it uses, but it's open-source and multi-platform, so help yourself.

It has a configuration option ("limit CPU use to X%"). The way I'd expect to implement that is to use platform-dependent APIs like clock() or GetSystemTimes(), and compare processor time against elapsed wall clock time. Do a bit of real work, check whether you're over or under par, and if you're over par sleep for a while to get back under.

The BOINC client plays nicely with priorities, and doesn't cause any performance issues for other apps even at 100% max CPU. The reason I use the throttle it is that otherwise, the client runs the CPU flat-out all the time, and drives up the fan speed and noise. So I run it at the level where the fan stays quiet. With better cooling maybe I wouldn't need it :-)