Just like the box on the 1040 tax form that allows taxpayers a choice about whether their money will go towards funding presidential campaigns, perhaps there should be more options.
How about a box on whether to give money towards Embryonic Stem Cell research? No longer could the opponents of funding it say “not with my tax dollars!” Those who are adamantly opposed to the idea do not have to fund it.
Those who qualify as Conscientious Objectors to war could choose to use the share of their money that would have gone to the military towards a beneficial domestic program of their choice.
100% control over where your taxes would go would probably be a disaster, but if made it something like 25% of your taxes you could directly control, I think it would be a good thing.