Let's start with a simple truth: The Constitution is a document meant to limit the power of government. If you cannot agree with this axiom, read no further, as there is not chance in the world you will agree with anything that follows.
The Commerce Clause is one of the Enumerated Powers in Article I of the Constitution. Even the granting of powers is, in a sense, a limiting of powers, becuase by declaring what Congress may do, the framers were implicitly declaring what Congress may not do. This, by the way, is the point of the Tenth Amendment, which is conveniently ingored by 99.99999999% of everyone involved with the governance of this country on a national level.
The Commerce Clause, properly interpreted, is a tweak. The Articles of Confederation, which preceded the Constitution (think of it as Constitution 1.0) had several problems, one of which was that each state could prevent or hinder other states, and/or individuals from those states, from doing business in or through the state. Imagine trying to run a courier business when you had to stop at every state border, submit to inspection, pay fees (or bribes), and generally be swallowed up in red tape to the point you could no longer do business. This was happening, and this is why Congress was granted to regulate (that is, make regular in the sense of making uniform and consistent) commerce between the states.
Over time, however, Congress has managed, along with the help of it's co-dependant enabler the Supreme Court, to mangle the meaning of the Commerce Clause in ways to grant itself virtually unlimited power to do anything. The "logic" used, to horribly oversimplify decades of twisted jurisprudence, goes something like this:
Premise: Commerce involves transactions between people
Premise: Congress can regulate commerce (where regulate means "control" rather than "make regular")
Conclusion: therefore Congress can control people.
Throw in a little dash of "Necessary and Proper" from elsewhere in Aricle I, and you have a recipe for unchecked government. Of course, if you happen to be politically aligned with the current congress, this probably doesn't bother you much. If you're not, then you see where this can go wrong.
The egregious example of overreaching that always come to mind when I think about the Commerce Clause is Wickard v Filburn, in which the Supreme Court decided Congress has, in the name of regulating interstate commerce, the authority to prevent a farmer from growing wheat on his own farm for his own consumption.
Let me repeat that, in simpler language: A farmer can be prosecuted for growing wheat to feed his family. Such an absurdity should, on its own and with no further analysis, be a signal to any competent judge that something is wrong. Yet Wickard has been controlling federal case law for seventy years.
The Commerce Clause is the dirty little secret of American politics. The Supreme Court has made baby steps toward forcing Congress back in to a sane interpretation (Morrison most noteably), but not much real progress has been made. The Obamacare ruling, expected in June 2012, will have a sizeable Commerce Clause element in it. Such a big case could decide how future Commerce Clause cases are going to go for year and years.