I agree with pohnpei, the Declaration was a guideline, and other documents by our founding fathers developed these ideas further. Anything can be tied back directly to one of the three mentioned rights: religion, gay marriage, etc. I did not know John Locke's addition, but I wonder now, why our founding fathers changed the original idea of Locke's.
I would not include any other rights because the Declaration of Independence was not supposed to be an exhaustive listing of the rights that we have. Instead, it was supposed to be a general statement of what sorts of rights people have.
In the Declaration, we are told we have the rights to life, liberty, and the pursuit of happiness. I would argue that any right that you can think of would be included in those three broad categories. For example, both the right to freedom of religion and the right to bear arms could be included under either liberty or the pursuit of happiness.
I guess if I had to pick a right, I'd pick "property." This was one of John Locke's original set of natural rights that he said all people have -- life, liberty, and property. Jefferson changed that and put "pursuit of happiness" in instead, but I think that the right to hold private property is one of the most important rights that we have as human beings. Of course, it can be put in either liberty or the pursuit of happiness. But if I were forced to put another right in the Declaration, it would be the right to own property.