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There are different types of 3.5mm jacks.
- 2-pin connectors exist for mono audio but one rarely comes across them these days
- 3-pin connectors carry stereo audio in only one direction (in OR out)
- 4-pin connectors exist for stereo out with one extra contact for microphone
Each jack plug need to be used in combination with the correct socket. Image below for illustration purpose only. It does not cover all possible layouts:
To make it more complicated there are different ways 4-pole jacks are wired between different equipment manufacturers. But this is the whole another story...
Answering your original question, it is probably the case that your PC manufacturer has equipped your machine with two separate ports for microphone and audio out. One can only speculate about the reasons why the PC was designed like that. Could have been any of the following:
- Manufacturing cost
- Compatibility with standard headphones
- Compatibility with standard speakers as pointed out by @Randy Orrison
- Combination of the above
- Something else...
Comparing with USB is not strictly correct. First of all USB is a digital interface while 3.5 mm jack is analogue. Having that said, USB can carry multiple signals across the same wire. Also if you look closer at USB connector (type A most commonly found on PCs) you will see that there are 4 contacts inside...