For example, to put an apple tv to sleep you must press and hold the play/pause button for a couple seconds. How would I do this with a universal remote (or which ones can do this if any)?

I have not bought a remote yet but was looking at a URC MX-350... can it do this?

HI if you are wanting to put the ATV a Sleep to save power your wasting you time there is no benifit, it has almost the same power consumption.

I use a relay to cut the power to my ATV to turn it off, that saves 100% power :)

Menu // Ensures the aTV is in a state which will allow for forcing it back to the Main Menu.
Delay 1.00 sec
Menu (IR duration set to 3.00 seconds) // Forces the aTV to return to the Main Menu.
Delay 1.00 sec
Select/Play/Pause (IR duration set to 3.00 seconds) // Forces the aTV into "Standby" mode.

An apple tv was just one of the devices I need a press and hold for but thank you for letting me know it does not save much power. Anyways, I can not find IR Duration anywhere in the manual for the MX-350. How would I go about setting it?

Unfortunantly you can't specify macro command duration on the MX-350.

can you suggest a remote that has this capability?

pronto Tsu9200 or TSU9300

With URC, any of the MX-900 or above will do it, I believe.

At least with database codes.

This is just speculation on my part, but it appears to me (looking at an upgrade file at hifi-remote.com) that the Apple long press doesn't send a signal of long duration. Instead, apparently it simply sends a short signal when the key is let up. If the press was a short duration, then it sends one IR command, and if the press was long, it sends a different IR command.

If that is true, then you can teach any learning remote the two commands (to different buttons, of course). Probably pretty easy to check by looking at the output of the Aple remote with a digital (e.g. cell phone) camera, and seeing when the IR is being sent, and if it lasts for a long time.