Tim,
Like you, I never payed those little boxes any attention until recently. As Steve says, when used properly it is a very good tool especially for the nubee who doesn't know any of us from Adam's house cat. It gives him some guide as to how much confidence he can put in someone's advice. Not a perfect gauge, but for the new guy, it's the best he's got for a while. Once he has been here a while, he can develop his own opinion on who provides information that is relevant and accurate for him.
I will say that with all the frapp about multiple IDs, the misuse and abuse of the reputation system has had as much, if not more, impact than the existence of the multiple IDs. It is the fact that multiple IDs were used to subvert the purpose of the reputation system by carrying out personal vendettas using the system as a weapon. That is not why it is there! Ding someone if they repeatedly give bad or wrong advice; or, if they state opinion or theory as fact without clearly identifying it as such, as in "IMHO." In the same vein, if someone repeatedly supplies you with good information that would have taken you 10 times as long to dig out, reward them with some brownie points with the thought in mind that you are saying, "new guy, pay attention to what this fellow says: he knows his $#!+."
From what we can tell, the abuse has been minimal. But, we are paying more attention to what happens (BTW, all reputation actions are recorded by the forum software, so there is no doubt about who is doing what to whom.) If it appears that the system is not providing its intended benefits because of misuse, it will just be turned off. That would be a shame because it can be a valuable tool.