I do think that the rep system works, pretty much, given that you should be posting accurate reasons for WHY that Rep was given.
I don't ever expect to be given Rep for my advice or my behaviour. It's a nice bonus, and makes me feel warm and fizzy when it happens.
I will only rep someone if they have done something out of the ordinary, or brightened my day. Marlowe got rep added because he is a great contributor to these forums. I actually felt guilty when I got a rep point back in return, because I didn't feel I deserved it.