I think the reputation system needs to be done away with entirely. I think it is a tool for cowards who were owned in a discussion/debate and have no logical response and those whose skin is so thin that they cannot handle seeing an opinion different from their own.
If the reputation system stays, it should be modified to allow people to know who exactly is behind it. Without anonymity to hide behind, the cowards who neg rep people for no good reason will stop since it is not in their nature to do anything in the open. I think this forum will become a much happier place when that happens.