K Street Mole has a great post about the two remaining candidates. Here is one difference I hadn't thought of.
Supply side tax cuts: McCain doesn't believe that lowering taxes helps the economy and ultimately boosts government revenue (opposed the Bush tax cuts); Huckabee supports pro-growth tax-cutting policies, recognizing they make the U.S. economy more competitive internationally and help create jobs.
I encourage you to go read the rest of it yourself.
I just got the FRC voter guide. Here are the differences between Mike Huckabee and John McCain according to them.
Bioethics/Stem Cells and Embryos
Mike Huckabee would not permit federal funds to be used for leftover embryos derived from in vitro fertilization or embryo destruction research. John McCain would.
Mike Huckabee would support a federal law prohibiting states from engaging in research in which a human embryo is destroyed. John McCain ?
Promoting Stronger Marriages
Mike Huckabee would support a U. S. constitutional amendment to define and Protect marriage as the union of one man and one woman. John McCain would not.
Mike Huckabee supports legislative initiatives that emphasize border secutity. John McCain does not.