I would say the biggest cost is the loss of lives during the war on terrorism. I would also say that we have given up some of our freedoms as someone else mentioned.
The war on terrorism has made many other nations view the United States in a not so positive way. In addition, traveling is a lot more of a hassle, although I have to add that I do feel safer when I fly on an airplane. This is not really because I am afraid of a terrorist attack, just people who are idiots in general. Also, people of middle eastern descent seem to be targeted because of the color of their skin.
The rise of the idea of "report any suspicious activity," the announcement we hear in airports, train stations and elsewhere. This is a disgusting way of making people distrustful and suspicious of everyone and everything. Just another stress to add to everyone's lives.
Another is the increase in the willingness to always see things as us and them, one side and the other, right and wrong instead of different and interesting and worth learning about or talking to. If we spent half the time and effort and money we spend on useless security measures that just make everyone hassled and frustrated on things like understanding people different than us, we'd likely be a whole lot better off.
1. loss of our once proclaimed slogan: Land of Opportunity (now we seem to be telling all immigrants, stay out.)
2. loss of time - due to heightened security measures
3. loss of trust - in our nations leaders, the media, public transportation, strangers, forgotten backpacks
Three non economic costs of the war on terrorism include a) the loss of so many soldiers who enlisted to serve and ended up dying in service b) the disruption to our safety and security in airports, since now it is virtually impossible to fly in peace c) the loss of civilian lives in the places that have been struck. From schools to temples, very important and essential places had been destroyed in Iraq and Afghanistan. And still, nobody has found Bin Laden. THAT is the biggest cost: The shame of us not to have made him pay for what he did.
I guess the main non-economic cost of the war on terrorism is in the loss of freedom that we experience as a result of that "war." For example, we are much less free on airplanes these days than we once were. We cannot bring liquids on board, for example. We are less free in the airports and cannot go with our loved ones to see them off at the gate.
I think another one is the loss of trust that we have in each other. This is less closely tied to the war on terror but it is affected by that war. We are taught now to be suspicious -- to always be on the lookout for people behaving strangely. It's like a loss of innocence.
Finally, you can argue that it is reducing the standing of the US in the world. Some people say that we look less like moral leaders of the world given how we are prosecuting this war.