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A lot of the differences have to do with church organization. Thus Episcopalians had bishops. Presbyterians had elders, and no bishops. The Independents and Separatists who later became Congregationalists tended to oppose overarching hierarchies and church organizations and rely on the judgement of the individual congregations, hence the name they adopted. Theology was affected by the dispute, though, since the weaker the church hierarchy the more likely a denomination was to accept the more radical Calvinist views of the day (16th and 17th century).

Nationality or ethnicity was also important: Lutherans and Episcopalians are historically not so very different. The Lutherans were the Continental (Germany, Scandinavia) equivalent of the Anglicans (who became Episcopalians in America), in so far as they both stood between Catholicism on one side and the radical Protestantism of the Calvinists (Presbyterians and Congregationalists in Scotland and England). The Presbyterians (Scots and Scots-Irish) shared much theologically with the French Huguenots, and the Dutch, German, and Swiss Reformed, their fellow Calvinists.

Social class was also important. Methodists were an evangelical outgrowth of Anglicanism/Episcopalianism at first. They were yeoman and tradesmen who had little patience with the rites and rituals of their upper class co-religionists, and eventually the two churches grew apart. As Americans move up the social ladder they tend to move from Baptist to Methodist to Presbyterian to Episcopalian, though there are plenty of exceptions.

A once very strict faith like Congregationalism, tended to become far more liberal as its members grew wealthier. The most liberal and least orthodox became Unitarians and Universalists, and the same process continued to take many Unitarians entirely out of the Christian or Theist camp. By contrast, the Baptists, once the theological "left-wing" of Christianity, have become quite conservative over time. Individual reading of the Bible was regarded as a radical and unsettling idea half a millennium ago. It still is, but today the sources of radicalism are secular, and denominations that attach the most importance to the wording of the Bible are reckoned old fashioned or "reactionary" by the secular media.

None of this is intended to minimize the real credal differences that separate various denominations or the real faith that they share. It's just to suggest that sometimes differences are more apparent than real.

If you're interested in where you might fit in, there are plenty of quizzes on the Internet (like this one) that can give you a clue. It's best to try to find out as much as you can first, rather than just choose the answers you like, though.