My understanding is that the control qubit in a controlled-not gate remains unchanged after the controlled-not operation is performed on a target-qubit (so the Pauli-X gate is performed only on the target-qubit, and nothing is done to the control qubit). Such that, if the control-qubit is measured later, it would have the same value as though it had never acted as a control-qubit.
That understanding seems to be supported by most of the materials available, and by, for instance, the first few minutes of this video: http://www.youtube.com/watch?v=rLF-oHaXLtE
However, I find two quantum computer simulators which produce results contrary to my assumption, wherein the control-qubit appears to be modified by the CNOT gate in certain circumstances.
There is a nifty quantum computer simulator here that I suggest you use to see what I'm talking about. It runs in your browser and doesn't need Java or Flash (it's HTML5): http://www.davyw.com/quantum/
Here is the setup code: On the webpage, select the [Workspace] Menu, then select [Import JSON] and paste in the following code to set up the example circuit:
The results of psuedo-measurement return |00> and |11>, however, shouldn't the first qubit always be 0 when measured, even if it is in fact a control-qubit, since the control-qubit remains unchanged regardless of what the target qubit's value is? The second hadamard gate should just reverse the first hadamard gate, meaning whatever value that qubit was initialized with (|0>) should be be the same upon measurement (|0>) -- which is what happens when the CNOT gate is not present.
Why are these programs flipping the first qubit, the control-qubit, in some cases?
The second quantum computing simulation program that does the same is: QCAD 2.0 (qcad.sourceforge.jp).
Note: In the webpage simulator linked, you may remove the CNOT gate by right clicking on it, and you will observe that running the simulator (by pressing [ENTER]) produces 0 for all possible measurements of the first qubit as expected, but with a CNOT in place and the first qubit as the control-qubit, placed mid-way on the circuit between the hadamards, the first qubit sometimes measures 1 according to this simulator (press [ENTER] to see the adjusted measurements).