I can think of a better system for doing the good that earmarks do, but since everyone seems to assume unthinkingly that they are bad, I want to put my hands up for the good they do.
"Earmarks" are basically add-ons to legislation that are often tangential to that legislation. They are currently under fire because 1) they seem sneaky, 2) they are associated with "special interest groups," and 3) the current libertarian atmosphere. They seem sneaky because they are like the little fish that attach themselves to whales. You want the whale, not the Remora attached to it. But because you want the whale, you take the Remora too. It's too hard to get legislation through to propose a bill just about that bridge that would bring commerce to the little island you live on. So you slip it in with something else.
Certainly special interest groups lobby for them. The ethanol companies in my state would sure love that tax deduction, and that will help my state's economy. Then there's the libertarian thing. Why should I as a citizen of Indiana be paying for some bridge in Alaska?
After saying all that, I oppose doing away with earmarks until some other system to replace the good it does is in place. The things these earmarks do are often the difference between the necessary and the beneficial. Can we live with the ferry taking us to the island? Yes. But how much better things would be if we had a bridge, and my state does not have the extra money to build it.
As far as the libertarian argument goes, the principle is that what goes around comes around. I may pay for your bridge today, but you will help my university tomorrow. We all become better together than any of us could be alone. This is the fatal flaw of libertarianism. The sum is greater than its parts.
I'm sure there is a better way to do it, maybe a pie from which every state received a certain percentage for these sorts of projects. But until something like that is in place, it would impoverish us to do away with earmarks. Cut them down? Absolutely. Be very careful about the ludicrous ones? Absolutely. But recognize the great value they have played in enriching America as a whole? Certainly.