Got the flood fill working, I stole the algorithm from some other code I had lying around. Only took about an hour to get it working. One aspect that was a little tricky is that QPixmap doesn't have a "getPixel" method, I had to convert it into a QImage to actually test the pixel values. However, when actually drawing the pixels, I can draw onto the target pixel map directly rather than having to convert the image back to a pixel map. (Actually, I optimized it so that it draws in horizontal strips rather than one pixel at a time.)
I also made it so that you can render the flood filled pixels onto a stencil bitmap. This would allow you to "floodfill" various pixel effects, such as brighten, darken, etc.
I also added a bunch more tool buttons to the tool bar - magnify, clip brush, pen size, etc. About the only thing left to do on the paint pad is the transfer modes. Once I get that done, I can work on the rest of the application.