The L5 Remote

L5 Remote is a $50 hardware attachment that, with an accompanying free app, turns an iPhone into a universal remote. It works with home entertainment devices that use IR (infrared) signals. It's also programmable, so you can delete buttons you don't use and save and back up different remote configurations you create.
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Peel TV

Peel's universal remote solution for the iPhone and the iPod Touch costs $99.99.
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Dijit Universal Remote App

Dijit Universal Remote App is a free iPhone app that can control some connected devices in your entertainment system, including the Roku set-top box, with no extra hardware needed. You can also update your Netlflix queue, discover new shows, and make recommendations to your social networks.

Dijit has also partnered with Griffin to work with Beacon, an IR blaster that sits near your TV. That lets your smartphone talk to your TV and other devices that can receive only IR input. Dijit's plan is eventually to have direct access to a host of Web-enabled TVs, TiVo, and other entertainment devices without need for the Beacon.

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Samsung Android app

Samsung has an accompanying app that lets owners of a Samsung Web-connected TV control their set from an Android phone.
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Remote

Apple makes the Remote app for the iPhone and the iPad that allows gesture inputs to control Apple TV and iTunes.
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My TV Remote

My TV Remote is a $10 round dongle that plugs into an iPhone. The accompanying free app enables users to create customizable remote buttons on screen for TVs and a variety of set-top boxes. The app also allows users to search shows in a program guide on the phone, see what friends are watching, chat with friends in the app, and comment on the shows.
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