This is from my answer here. It sparked some interest, and I felt it should have its own discussion.
Background - The Problem with Reputation
As it stands, reputation surrounding community wiki (CW) questions can be unfair or even inconsistent. This would be fixed by removing reputation gained by posting CW answers, regardless of when they were posted.
Consider when a person asks a question that should be CW, and is only later changed to match this status. Often times, people will post their answer as non-CW, often to try to get a bit of reputation before the question is migrated to CW.
Once the question is made CW, any further answers will not generate reputation. This creates an inconsistent state of reputation, where people have earned reputation off of CW questions, which should be impossible.
Arguments For Reputation
One argument was "the intent of the author was for it not to be CW". Of course, this means we would have to never change the CW status of a question and assume the poster always intends correctly. There is reason to be believe this isn't always the case, though. Sometimes the CW status of a question needs fixing, and answers should match.
This would cause a bit of rep loss for myself and others, but I feel it would create a more consistent representation of reputation. Community Wiki questions are questions that do not affect reputation at all, and then we have regular questions.
In short, I consider the ability to keep reputation on a previously non-CW question a loophole. Loopholes, while resembling free-hand circles, are generally not good.