As an openly Christian political scholar, I get asked this question a lot. People want to know if it is somehow morally acceptable to vote for someone of a different faith. To try to answer the question, the Bible does not deal with this question directly (seeing as how there wasn't a lot of voting going on back then). I tend to hear two different arguments on this issue. Those who argue that we should only vote for Christians claim that voting for non-Christians is equivalent to being "unequally yoked". Those who say that voting for non-Christians is acceptable cite the passages that tell us to be good citizens, no matter who is in charge.
Personally, I don't find either argument particularly persuasive. I don't see how voting for someone is being yoked to them. One might argue that choosing someone as your leader is being yoked to them, but then the command would have to be interpreted as saying, "If the leader of your government is not a Christian, then you have to move because you can't be unequally yoked." Back in the days when none of the government leaders were Christian, this reading of the command would have been problematic.
Regarding the second argument, the commands are to be submissive to governmental leaders, even if they are non-Christian. This does not necessarily condone actively participating in the selection of a non-Christian to lead you.
Since we don't seem to have any specific Biblical guidance in relation to voting, what are we to do? There is a book I read back in college that I think provides a good, biblical, understanding of what to do in these situations. It is Decision Making and the Will of God by Garry Friesen and Robin Maxson. Their central argument (for purposes of this discussion) is that Christians are given broad principles of guidance through the Scriptures and, when specific situations come up that aren't directly addressed, we use wisdom to make a decision based on the broad principles.
So, on this view, we should look at broad principles in the Bible, pray about them, and use wisdom to decide who to vote for. My personal view on this (and feel free to disagree with me) is that it is perfectly justifiable to vote for a non-Christian if the non-Christian will do a better job of advancing the principles found in the Bible.
I have a slight advantage in saying this. I've personally met a lot of these "Christian" politicians, and I can safely say that there frequently isn't a substantial difference between the Christian and non-Christian in how they live their lives or how their faith influences their political activities. All other things being equal, I would rather vote for a non-Christian who is at least open about the fact than vote for a "Christian" who is only professes faith for appearances.