Sapper, I know this isn't supposed to be about how to change it, but this topic is a senstive one for me, so I can't resist venting.
I have been arguing for many years (but nobody listens

) that the President should issue an Executive Order directing federal employees NOT to implement earmarks that are contained in any report language accompanying the actual legislation. In other words, unless an earmark is expressly written into the legislation that the President signs, it should be ignored.
As it stands, the Committee and personal staff in Congress badger the federal employees to implement all the obscure earmarks that are advocated by lobbyists and inserted/buried in committee and conference reports accompanying the legislation. They use the implicit threat of retaliation (in the next funding cycle) to get the earmarks implemented.
The funny thing about earmarks is that they generally do not provide additional funding to the Agency or Department. Any money spent on earmarks is money that can't go to the Agency's priority programs.
There may be hope, though. In his State of the Union address on Monday night, President Bush seemed to indicate that he might do exactly what I suggested above in the coming budget cycle. This would finally take the onus off the federal employees who have to continually deal with the lobbyists and congressional strong-arming. They would be able to respond by citing the E.O. prohibiting them from implementing the obscure earmarks.