Sleep timeout missing from the energy saver preferences

Deliberately Removed

Apple have removed the Computer slider from the Energy Saver settings. This is deliberate.

The decision is related to Apple's introduction of improved hardware, Power Nap support, and the engineers' belief that OS X is best placed to manage the computer's power state.

If you would like to see this slider return, provide feedback to Apple.

Downloads and Other Long Running Tasks

OS X will stay awake during most long running tasks.

The behaviour will depend on the software downloading the file. Safari and Transmission, for example, both ask OS X to stay awake while a download is ongoing.

Applications need to lodge power assertions with OS X that explicitly stop the computer sleeping. You can see these assertions using the following pmset command:

pmset -g assertions

For older software, you can add this behaviour using the built-in command line tool caffeinate.

Third Party Alternatives

Third party tools exist to supplement the Energy Saver settings. I created Power Manager and it can put your Mac to sleep after inactivity.

Other tools exist and you could probably create a script to also recreate this behaviour.

Basically, Safari will download the file but it will not go to sleep.

You can also check the box that says "Prevent computer from sleeping automatically when the display is off." I have that box unchecked; power nap really, in this case, does help. I've actually ended up answering one of my own questions by reading this thread.