There are a few ways to turn your smartphone into a universal remote for your home theater system.
First, check the Google Play Store or Apple App Store to see if there are apps for your home theater components. If your home theater component connects to the internet, there’s a good chance there’s an app available for your smartphone. Many modern audio video receivers, TVs, and set top boxes have apps.
If you’re not able to get apps for all of your components, you may want to consider the Logitech Harmony Universal Remote. In addition to the Harmony being a remote itself, it comes with a hub and smartphone app. The hub sits at your home theater system and connects to your home network. Then, when activated by the app, the hub will send an IR signal to your components.
If you have a computer hooked up to your TV, there are apps you can use to avoid using a keyboard and mouse. The Logitech Touch Mouse is a good solution for this. First install the Touch Mouse to your media PC, then your phone can control things using the free iOS app. Another similar option for Android is Remote Trackpad.
If you’ve made a Mac Mini media center, Remote Buddy is a great Mac OS X program that brings lots of control to your Apple remote or smartphone via an AJAX web app. Remote Buddy costs about 20 Euros.
For more information on turning your smartphone into a universal remote, watch episode 55 of Know How on TWiT.tv.