Well I put 'pokemon fusion' into Google and this site came up: http://alexonsager.net/pokemon/
So maybe you can do what you wish there.
Otherwise you will need a graphics program. Maybe try paint.NET, which you can get from http://www.getpaint.net (it's free). Then you can open images and copy-paste parts from one image to another, or draw pixel-by-pixel if you want.
edit: here's a video on YouTube that says how to do it using Microsoft Paint: http://www.youtube.com/watch?v=944l6mBv3Ew