Universal remotes appeared on the market decades ago, but have always been a challenge to setup with all your devices (even with today’s remotes that can be programmed much more easily). Plus, the setup options may not be ideal for your mix of devices. Using your smartphone as a replacement is a great option.
Apple pioneered this concept with the iOS Remote app that can control the iTunes library on your computer or an Apple TV. That app/hardware combination works really well. But Apple’s app uses Wi-Fi where most home theater devices use old school IR signaling. The solution is either a combination of smartphone app (there are several to pick from on virtually every platform) and a small IR device that communicates with your smartphone over Bluetooth/Wi-Fi or a small IR dongle plus app for the device.
Which solution you choose will be dictated by your smartphone. iPhone users should check out NewKinetix, ThinkFlood's RedEye app, and Sonos controller. Android users can take a look at RedEye for Android, also from ThinkFlood, and BlackBerry users should have a look at AV|Shadow.