The AppleTV is an awesome little piece of equipment considering what it allows you to do. It's sleek and small. The remote is just as sleek and small, unfortunately that makes it CRAZY easy to lose one.
So, you've lost your remote... now what?
Luckily, Apple thought ahead. The AppleTV has a remote learning function onboard and it's ridiculously simple to set up. In other words, you can use your TV remote(or DVD, Bluray, etc) as your AppleTV remote. It takes a total of about four minutes to run through the prompts and you're done.
On your AppleTV, go to the settings app. Select General, then Remotes, followed by Learn Remote. (Settings > General > Remotes > Learn Remotes) The prompts will ask you to press a button on your remote to represent the selected button on screen. The AppleTV remote has the directional up, down, left, right, select, back, and play/pause buttons. You'll be able to assign all of these except for the play/pause button.
Here's the thing, you can select any button to represent the selected function (as in you can have the AppleTV learn that your TV remote's volume up button is the "left" directional button, so choose wisely). Personally, I just chose the directional buttons on my TV remote to represent the same in the AppleTV (with the TV's return button being the back button).
"But dude... I lost my remote. How the hell am I supposed to get through the menus??"
Well if you don't have the Remote app on your iDevice, then go download it now. Once downloaded, use it to navigate the menu until your new TV, DVD, Cable Box remote is learned in your nifty AppleTV.
Hate having all those damn apps on your screen that you've probably never even opened? On your AppleTV remote, hold down the select button to make that app "wiggle" (just like on your iDevice). Once it's wiggling, you can press the Play/Pause button to hide it from the main screen.
Also - once you get an app to "wiggle," you can move it around in the same way you can move an app on your iDevice.