I've had a few complaints (probably 5 or 6) about how I give out negatives reputations. I've also had one person who's thanked me for a negative reputation that I've given them. I've only had one comment about a positive reputation. I beleive that I give out about 2/3rds approve and 1/3 disapprove. I also leave comments on 90% of my comments, and 99.9% of my negatives
The way that I give out positive reputations is fairly nebulous, but the largest factor is how much reputatation you already have. I hold people with high reputations to a much higher standard if they want to get a positive reputation from me. The way I give out negative reputation is more defined.
- If something you post is wrong, and you provide no supporting information, you get a negative.
- If I have to think really hard to understand what you are saying, you get a negative (this mostly involves spelling and grammar).
- If you post with a negative attitude, you probably get a negative.
- If you post something in the blatantly wrong forum, or multi post a thread, you get a negative
- If post says nothing of value (and it's a technical type forum) you get a negative
- If you comment about a reputation you received publicly, you may get a negative (This thread is an exception, because it is designed to talk about reputation). Take it to PM or IM, and if something is really bad, let Brandon know, in private
- If you post a controversial topic, without it being the time or place to discuss it (or you being the correct person to post about it), then you probably get a negative.
Hopefully that clears up every negative I've given (and now I can point angry people to it, rather then explaining it to them when they are angry

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The most important thing to remember is that reputation levels out. There are many more people here who respect your opinion if it is well reasoned, then give out negative reputations if they disagree. If you all you see is a few random negative reputations, then don't worry about it. If you see a consistent trend, hopefully they left comments and you can think about what was said.