The Apple Remote is a slick little gadget, but Apple made a particular design choice that annoys the bejebus out of me: out of the box, every Mac is set up to work with any Apple Remote. If you have a couple of sleeping MacBooks in your living room like we do when you pick up a remote to watch something on the Apple TV, you could very well wake all three devices with the press of a button or two. To make matters worse, Apple isn't very forthcoming about solving this problem or giving you an easy way to bind an Apple Remote with one device or another. Fortunately, there are a few options that aren't hard to pull off.
Your first choice is to completely disable the infrared receiver on your Mac. If you rarely or never use your Apple Remote, you can disable the infrared port on your Mac so it simply no longer accepts signals, intentional or otherwise. This is done with the setting you see above, accessible at the bottom of the Security Preferences Pane.
Your next option is to pair your remote(s) with their respective devices, a step that I wish Apple could somehow implement from the get-go so you don't have to. Here is an Apple support doc detailing the one simple step to pair an Apple Remote with a Mac, and another on pairing and unpairing a remote with an Apple TV. In case you ever have to unpair a remote from your Mac, you can simply open the Security Preferences Pane and click the Unpair button at the bottom right (note that this button is only illuminated when an Apple Remote is actually paired with your Mac; otherwise it's faded out).
For your sake, I hope you don't have too many Apple Remotes to pair, but this should solve those sudden waking moments for your Macs.