I was thinking about this earlier and thought I'd ask. Can third-party remotes be used with the Apple TV (any and all versions)?
Yep. You can have your Apple TV learn the remote codes of any IR remote by going to Settings > General > Remotes. It will then ask you to hit buttons on your new remote corresponding to what it shows on screen.
Full instructions can be found at Apple's site: Controlling Apple TV with a third-party remote control