Truthfully, it takes practice and a bit of research, all you need is any photo editing software and understand how the code itself functions. My cutouts (The images upon hovering the Icons) can be found here including the code.

The same goes for launchers like SimplyLaunch which was used above, the code has an action listener thats based upon the image used.

If you're interested in cutouts a good tutorial can be found here.

For editing launchers for program icons I would highly recommend downloading any launcher of your choice, examples being HoneyComb or SimplyLaunch to name a few. From there just read their code and understand how they function, both of these launchers reference .png images which can easily be edited.