The whole list or just the top ten?
1. The state should not be financing churches. In the US, the government finances churches through the faith based initiatives. Here's more information on this donkey that you have to pay for through your taxes like it or not regardless if the church beliefs or plans gel with yours: http://www.hhs.gov/partnerships/ I'm sure if as an atheist you tired to use these programs you would be turned away or preached at. A person should not have to be preached at or turned away from a government sponsored program due to their lack of faith.
2. Who decides what churches meet the muster and which don't? Polygamy is not popular in this country, but practiced by many religions elsewhere. For a number of years, polygamists have been singled out as not good by the US government. The government claims to be hands off churches until it comes to polygamists and often Muslims. Churches should be treated the same, but they aren't. The good ones get government money to finance their pet projects, the bad ones get a lot of scrutiny and sometimes harassment.
3. IMO, if we truly had a separation of church and state, ministers and churches would have to pay taxes. Perhaps the biggest tax haven of them all is to declare oneself a minister. The government doesn't check up to see if someone has actual followers or actually funds programs to help the poor, etc. From what I can see, most ministers pay no taxes, live in a church owned home and basically get off scot free in the tax department while they live pretty lavish lives. Remember the Bakers? Why should a Walmart worker have to pay taxes while a preacher making 6 figures does not because he's "a man of god"?
I'm tired right now, but I'll have more later. Basically, I feel as an atheist, I shouldn't have to support the lavish lifestyle of a baptist preacher through my taxes and I shouldn't have to live under the laws of his church. Right now, I think there are a number of people who would like the US to be a theocracy, however, they never think about what happens if their church looses out and they get stuck having to live under the laws of a church they don't like, and don't agree with. It's all well and good as long as it goes their way, and they never think what if it doesn't?
Have a look at my treatise: What is Secularism and why is it important?
You might want to check Youtube for the Eddie Tabash presentation @ the 2007 Atheist Alliance International (AAI) Conference...
It would be interesting to rank all the countries of the world by how strongly they separate church & state and see what you get. At the "no separation" end of the list, you'll have countries like Iran, Pakistan, ... I've often thought about showing this those Americans who are opposed to the separation.
I think I'll do a bit of googling now to see if someone's already done this.
I think Sam Harris' book _The End of Faith: Religion, Terror, and the Future of Reason_ may talk about reasons for separating church & state. I'll try to pull that book off the shelf tonight.
Michelle Bachman and Saudi Arabia come to mind as examples of good reasons.