When I'm working on any of my cartoon features, the process is pretty much the same. I sketch the toon, ink, and then scan. Often times, the scanned image may not align as straight and square as I need it to be.

Rather than take the original art and reposition ( and reposition and reposition,etc.) on the scanner's flatbed, I merely use Gimp's Rotate function. It's very easy and straightforward. Just select the rotate tool from the tool box on the left hand side.

Click the image and the rotate dialog box appears. Now, you can either rotate the art by moving your mouse over and around the image, or control the rotation in the dialog box with the slider tool.

You can see from the numerical output how much rotation is being applied centering, etc. Once you have things aligned, click “Rotate” and you're done!