Photographing your own children, even when you photograph children for a living, is definitely a challenge! Just like with everything else, our own kids act up most, for us. I've found some things make it much easier to get my little guy to cooperate, and even have fun!
When I want to photograph my son, it's easiest to let him just be himself; running around, playing, fighting imaginary villains, etc. My son loves to be the center of attention, so when I'm watching him, or we're playing together, is the best time to get the camera out.
I never try to force taking photo's on him; I want him to have fun when I'm photographing him. I don't want it to become a negative experience. If he doesn't want his photo taken, then I put my camera away. In my experience, if he has a bad time doing something once, he doesn't want to try it again.
When it comes to my own children, or my client's children, my favorite images, are always the unscripted, unplanned images. Children are amazing to photograph, and when you let them play and explore and just be children, the images are powerful. Their expressions are always more authentic, when they aren't being forced into them.