that completely depends on the specific cololeges you are interested in. For instance, when i visited MIT, they said they want a mathIC/IIC score, a science score, and one score of anything else. For example, if u had a 790 math IIC, a 800 chem, a 760 U.S. History, and a 580 Latin, then the 580 Latin would be ignored completely. However, if the chemistry was a 600, then it wold be counted, since they want the one science score (unless you had another science, such as biology).
Some other colleges want 2 or 3 of any type of SAT II. In that case if you had 6 tests, they would take the best ones, or whichever ones that you specify.