Oye11 appears to have noted the major differences. Of them, several are primarily liturgical in nature:
1) Methodists celebrate Holy Communion as a sacrament. I believe Baptists simply refer to it as an ordinance.
2) Baptists, as the name implies, make a bigger deal out of baptism than do Methodists. (Though that might be slighting the Methodist view of this sacrament some.) Most Baptists practice (usually adult) believers baptism by immersion and Methodist practice baptism of all ages (including infants who are presented by believing parents) by any of three means: immersion, pouring, or sprinkling.
3) While most people today probably couldn't tell the difference between a Methodist order of worship and a Baptist order of worship -- differeneces arising more out of personal preferences of the pastors than denominational issues -- the Methodist order of worship is based on a liturgy of prayers and the Baptist order for the service is based on a liturgy of the word.
Some of those liturgical issues, such as baptism, have theological roots based on different interpretations of a few key passages of scripture and whether church history and tradition are brought to bear in the decision making process or not.
One key theological difference is in the view of eternal security. Methodists believe that people have free will, that this free will is always a part of the nature that God created in us, and thus that people are always capable not only of sinning, but even of turning their backs on God and rejecting the salvation offered to us in Jesus Christ. (This is true not only for the unsaved but those who have already been saved as well.) Baptist theology is that God is sovereign and faithful that he will therefore never lose any that are placed in his keeping. Thus you hear the mantra, "once saved always saved". Yet, if one examines the Methodist concept of entire sanctification you will find that it results in the same outcome, though arriving at it from a different direction. Entire sanctification holds that as one grows in grace, one desires more and more the things of God and less and less that which is contrary to God's will in your life. Eventually (be it gradually or instantaneous not being an issue), by virtue of God's grace - not one's own righteousness, the process transforms the individual into one whose will exactly matches the will of God. In this condition they want for nothing apart from God and therefore would be just as eternally secure for they would never be inclined to exercise their free will to turn away from God. The remaining difference between Methodists and Baptists on this is that Methodist look at "saved" people who return to living lives of sin and say they are backslidden, and Baptists look on these people and suggest that maybe they weren't really saved the first time.