Your computer has a standard 5.1 surround soundcard on-board. This means that, in order to drive all 6 channels, you need 6/2=3 connectors.
- Green is the default stereo channel for front-left and front-right.
- Orange is the default sub+mid channel, sending audio to the subwoofer and the front-mid channel.
- Black is the default stereo rear channel for rear-left and rear-right.
Some onboard soundcards will send stereo output to the rear channel in case no connector is connected to the proper green connector. Other soundcards may simply up-mix the stereo sound to all channels to make the stereo sound come through all speakers.
The difference will be noticeable when you connect a 5.1 surround speakerset and you use/play a surround demo/movie. Then the rear channels will be mostly muted or have a lower volume in order to be able to get those channels played when audio comes from that direction.
Just for reference, the blue and purple connectors are input connectors, not output connectors. They are line-in and mic.