Universal remotes are pre-programmed or programmable remote controls that will control all the gear in your system. They come in two main flavors:
IR Remote Control
Most consumer mainstream electronics components come with IR (infrared) wireless remote control access. This system, while affordable, is the least reliable out there. It requires the consumer to have a direct shot from the remote to the component in order to execute a successful command. RF doesn't need this and RS-232 is hard-wired.
It is common for IR systems to use remote repeater systems that have an "eye" that sees the incoming command and distributes that command to the system accordingly. These repeater systems tend to be quite fragile, with flimsy wires and repeater eye stickers that don't effectively stick to the section of the components.
RF Remote Control
"RF" remote control of audio and video components refers to radio frequency. It is a superior way to control an AV component wirelessly over IR (infrared). The main reason this is an advantage is that it eliminates the need to have a straight line between the remote and the component receiving its commands. You can have a Blu-ray player around a corner and an RF remote will successfully speak to it, where an IR (without some sort of repeater system) will not.
Notable universal remote control companies include URC, Philips, and Logitech (Harmony).
Read reviews for the Harmony One Universal Remote and the Harmony 890 Universal Remote.