Pulsar Professional FX has a neat tip on their site for getting a really even toner transfer when making your own PCBs.
First, the PCB is cut to size, and the paper is tacked to the board.
Then, the PCB is placed paper up onto a dowel and rolled back and forth with the iron. Since the board bends slightly over the dowel the toner sticks evenly to the copper.
After that, just remove the paper as usual and etch with your preferred method.