The first thing you will probably notice after you open up your computer for the first time is that there are a lot of wires and cables inside, running in many directions. Fear not; there really is some kind of logic to this wiring.
There are several kinds of cables and wires inside your computer:
Power cables that carry DC power from the power supply to the motherboard, the fans, the disk drives, and other devices. The power supply often includes enough cables and plugs to provide power to more devices than your computer currently uses, so there are often spare power cables and plugs that don't connect to anything; it makes the inside of the computer neater and easier to work with if you can use a cable wrap or even a short piece of string to tie the unused cables to a rail or some other part of the internal frame. That extra cable is useful when you want to add a new hard drive or other component to your computer.
Data cables that move signals between the motherboard and the disk drives and other storage media.
Audio cables that carry digital audio between the sound card (or equivalent on the motherboard) and the CD or DVD drive, and from the motherboard to the internal speaker inside the case.
Control wires that extend switch contacts or LED indicators from the computer's front panel to the motherboard. Each of these wires has a connector at the end with a label that corresponds to a pin on the motherboard.
Signal cables that extend data and control signals from the motherboard to connectors on the front or back of the case.
If you can't identify a wire or cable by looking at it or by looking at the device or socket connected to it, leave it alone; it's almost certainly doing something important. The best place to find explanations for all the wires, cables, jumpers, and other settings on your motherboard is the manual supplied by the manufacturer, or the manufacturer's Web site.