Initially meant to be an indication of the level of helpfulness you, as a board member are . Reputation points are given by board members themselves and once you have accumalated a certain threshold of points, you will recieve an extra bar of reputation. Points may also be given out for other reasons such as humour or someone being in complete reason with the poster.
Green reps indicate positive points.
Grey reps represent positive or negative points which cannot be counted to your score because the person repping you is not yet "qualified to do so."
Red reps are negative rep points which decrease your current score because a certain memeber may be4live your post to be spam or absurd, amongst other possibilites. It is to be noted that bad reps are not in operation nowadays, a member may only gain positive points.