I moved this here into the feedback forum so that we didn't go off topic and so it may also be helpful to other members in the future should they have the same question.

Rep is forum of internet karma. A way to express a good post or one you disagreed with. For example. If someone makes a good post you can choose to give them rep (if you have enough rep power) by selecting the +Rep icon under your avatar.

Example:



You can do the same if someone posted something that you disagree with to the point where you feel like giving that person 'negative rep'. It's a simple feature, but can be confusing.

I'll try to dig up a better guide. I thought there was one in the FAQ, but there isn't.